From ce17af09b926c5d53a6a659a832cdffebbe6dabc Mon Sep 17 00:00:00 2001 From: Mariana Vertenstein Date: Fri, 14 Jul 2023 13:47:51 +0200 Subject: [PATCH 1/6] fixed problems encountered when using blom with CIME testing --- cime_config/buildnml | 139 +++++++++++++------------ cime_config/config_compsets.xml | 27 +++-- cime_config/testdefs/testlist_blom.xml | 19 +++- 3 files changed, 109 insertions(+), 76 deletions(-) diff --git a/cime_config/buildnml b/cime_config/buildnml index eecf5a68..e8c45153 100755 --- a/cime_config/buildnml +++ b/cime_config/buildnml @@ -30,6 +30,7 @@ set RUN_STARTDATE = `./xmlquery RUN_STARTDATE --value` set PIO_TYPENAME_OCN = `./xmlquery PIO_TYPENAME_OCN --value` set PIO_NETCDF_FORMAT_OCN = `./xmlquery PIO_NETCDF_FORMAT_OCN --value` set NINST_OCN = `./xmlquery NINST_OCN --value` +set TEST=`./xmlquery TEST --value` #------------------------------------------------------------------------------ # Check if HAMOCC is requested @@ -49,7 +50,7 @@ endif # Set RUN_TYPE to 'continue' if CONTINUE_RUN equals TRUE #------------------------------------------------------------------------------ -if ($CONTINUE_RUN == TRUE) then +if ("$CONTINUE_RUN" == TRUE) then set RUN_TYPE = continue endif @@ -75,14 +76,14 @@ set EXPCNF = "'cesm'" set RUNTYP = "'$RUN_TYPE'" set GRFILE = "'unset'" set ICFILE = "'unset'" -if ($BLOM_UNIT == cgs) then +if ("$BLOM_UNIT" == cgs) then set PREF = 2000.e5 else set PREF = 2000.e4 endif set BACLIN = 1800. set BATROP = 36. -if ($BLOM_UNIT == cgs) then +if ("$BLOM_UNIT" == cgs) then set MDV2HI = 2. set MDV2LO = .4 set MDV4HI = 0. @@ -101,7 +102,7 @@ set VSC2HI = .5 set VSC2LO = .5 set VSC4HI = 0. set VSC4LO = 0. -if ($BLOM_UNIT == cgs) then +if ("$BLOM_UNIT" == cgs) then set CBAR = 5. else set CBAR = .05 @@ -145,13 +146,13 @@ set JTEST = 60 set CNSVDI = .false. set CSDIAG = .false. set RSTFRQ = 1 -if ($PIO_NETCDF_FORMAT_OCN == 64bit_offset) then +if ("$PIO_NETCDF_FORMAT_OCN" == 64bit_offset) then set RSTFMT = 1 else set RSTFMT = 0 endif set RSTCMP = 0 -if ($PIO_TYPENAME_OCN == pnetcdf) then +if ("$PIO_TYPENAME_OCN" == pnetcdf) then set IOTYPE = 1 else set IOTYPE = 0 @@ -183,7 +184,7 @@ set EDDF2D = .false. set EDSPRS = .true. set EGC = 0.85 set EGGAM = 200. -if ($BLOM_UNIT == cgs) then +if ("$BLOM_UNIT" == cgs) then set EGLSMN = 4000.e2 set EGMNDF = 100.e4 set EGMXDF = 1500.e4 @@ -200,7 +201,7 @@ set REDI3D = .false. set RHSCTP = .false. set RI0 = 1.2 set BDMTYP = 2 -if ($BLOM_UNIT == cgs) then +if ("$BLOM_UNIT" == cgs) then set BDMC1 = 5.e-4 set BDMC2 = .1 else @@ -210,7 +211,7 @@ endif set TKEPF = .006 set SMOBLD = .true. set LNGMTP = "'none'" -if ($BLOM_VCOORD == isopyc_bulkml) then +if ("$BLOM_VCOORD" == isopyc_bulkml) then set BDMLDP = .true. set LTEDTP = "'layer'" else @@ -219,37 +220,37 @@ else endif # set BGCNML defaults -set ATM_CO2 = $CCSM_CO2_PPMV -if ($BLOM_RIVER_NUTRIENTS == TRUE) then +set ATM_CO2 = "$CCSM_CO2_PPMV" +if ("$BLOM_RIVER_NUTRIENTS" == TRUE) then set DO_RIVINPT = .true. else set DO_RIVINPT = .false. endif -if ($BLOM_N_DEPOSITION == TRUE) then +if ("$BLOM_N_DEPOSITION" == TRUE) then set DO_NDEP = .true. - if( $BLOM_NDEP_SCENARIO == 1850 && $OCN_GRID == tnx2v1) then + if( "$BLOM_NDEP_SCENARIO" == 1850 && "$OCN_GRID" == tnx2v1) then set NDEPFNAME = ndep_1850_CMIP6_tnx2v1_20180321.nc - else if( $BLOM_NDEP_SCENARIO == 1850 && $OCN_GRID == tnx1v4) then + else if( "$BLOM_NDEP_SCENARIO" == 1850 && "$OCN_GRID" == tnx1v4) then set NDEPFNAME = ndep_1850_CMIP6_tnx1v4_20171106.nc - else if( $BLOM_NDEP_SCENARIO == 1850 && $OCN_GRID == tnx0.25v4) then + else if( "$BLOM_NDEP_SCENARIO" == 1850 && "$OCN_GRID" == tnx0.25v4) then set NDEPFNAME = ndep_1850_CMIP6_tnx0.25v4_20190912.nc - else if( $BLOM_NDEP_SCENARIO == 1850 && $OCN_GRID == tnx0.125v4) then + else if( "$BLOM_NDEP_SCENARIO" == 1850 && "$OCN_GRID" == tnx0.125v4) then set NDEPFNAME = ndep_1850_CMIP6_tnx0.125v4_20221013.nc - else if( $BLOM_NDEP_SCENARIO == 2000 && $OCN_GRID == tnx2v1) then + else if( "$BLOM_NDEP_SCENARIO" == 2000 && "$OCN_GRID" == tnx2v1) then set NDEPFNAME = ndep_2000_CMIP6_tnx2v1_20200826.nc - else if( $BLOM_NDEP_SCENARIO == 2000 && $OCN_GRID == tnx1v4) then + else if( "$BLOM_NDEP_SCENARIO" == 2000 && "$OCN_GRID" == tnx1v4) then set NDEPFNAME = ndep_2000_CMIP6_tnx1v4_20200826.nc - else if( $BLOM_NDEP_SCENARIO == 2000 && $OCN_GRID == tnx0.25v4) then + else if( "$BLOM_NDEP_SCENARIO" == 2000 && "$OCN_GRID" == tnx0.25v4) then set NDEPFNAME = ndep_2000_CMIP6_tnx0.25v4_20200826.nc - else if( $BLOM_NDEP_SCENARIO == hist && $OCN_GRID == tnx2v1) then + else if( "$BLOM_NDEP_SCENARIO" == hist && "$OCN_GRID" == tnx2v1) then set NDEPFNAME = ndep_185001-201412_tnx2v1_20190702.nc - else if( $BLOM_NDEP_SCENARIO == hist && $OCN_GRID == tnx1v4) then + else if( "$BLOM_NDEP_SCENARIO" == hist && "$OCN_GRID" == tnx1v4) then set NDEPFNAME = ndep_185001-201412_tnx1v4_20180613.nc - else if( $BLOM_NDEP_SCENARIO == hist && $OCN_GRID == tnx0.25v4) then + else if( "$BLOM_NDEP_SCENARIO" == hist && "$OCN_GRID" == tnx0.25v4) then set NDEPFNAME = ndep_185001-201412_tnx0.25v4_20190705.nc - else if( `echo $BLOM_NDEP_SCENARIO | cut -c1-3` == ssp && $OCN_GRID == tnx1v4) then + else if( `echo $BLOM_NDEP_SCENARIO | cut -c1-3` == ssp && "$OCN_GRID" == tnx1v4) then set NDEPFNAME = ndep_201501-210012-${BLOM_NDEP_SCENARIO}_tnx1v4_20191112.nc - else if( $BLOM_NDEP_SCENARIO == UNSET ) then + else if( "$BLOM_NDEP_SCENARIO" == UNSET ) then set DO_NDEP = .false. set NDEPFNAME = "''" endif @@ -257,7 +258,7 @@ else set DO_NDEP = .false. set NDEPFNAME = "''" endif -if ($HAMOCC_SEDSPINUP == TRUE) then +if ("$HAMOCC_SEDSPINUP" == TRUE) then set DO_SEDSPINUP = .true. set SEDSPIN_YR_S = $HAMOCC_SEDSPINUP_YR_START set SEDSPIN_YR_E = $HAMOCC_SEDSPINUP_YR_END @@ -270,7 +271,7 @@ else endif # VSLS is currently only available for the tnx1v4 grid, since a climatlogy file for # short wave radiation is needed. -if ($HAMOCC_VSLS == TRUE && $OCN_GRID != tnx1v4) then +if ("$HAMOCC_VSLS" == TRUE && "$OCN_GRID" != tnx1v4) then echo "$0 ERROR: HAMOCC_VSLS == TRUE not possible with this grid resolution (no swa-climatology available) " exit -1 endif @@ -293,9 +294,13 @@ set SEDPORFILE = "''" # set DIAPHY defaults set GLB_FNAMETAG = "'hd','hm','hy'" set GLB_AVEPERIO = '1, 30, 365' -set GLB_FILEFREQ = '30, 30, 365' +if ("$TEST" == TRUE) then + set GLB_FILEFREQ = '1, 30, 365' +else + set GLB_FILEFREQ = '30, 30, 365' +endif set GLB_COMPFLAG = '0, 0, 0' -if ($PIO_NETCDF_FORMAT_OCN == 64bit_offset) then +if ("$PIO_NETCDF_FORMAT_OCN" == 64bit_offset) then set GLB_NCFORMAT = '1, 1, 1' else set GLB_NCFORMAT = '0, 0, 0' @@ -474,8 +479,13 @@ set MSC_SSTGA = '0, 4, 0' set BGC_FNAMETAG = "'hbgcd','hbgcm','hbgcy'" set BGC_AVEPERIO = '1,30,365' set BGC_FILEFREQ = '30,30,365' +if ("$TEST" == TRUE) then + set BGC_FILEFREQ = ' 1,30,365' +else + set BGC_FILEFREQ = '30,30,365' +endif set BGC_COMPFLAG = '0, 0, 0' -if ($PIO_NETCDF_FORMAT_OCN == 64bit_offset) then +if ("$PIO_NETCDF_FORMAT_OCN" == 64bit_offset) then set BGC_NCFORMAT = '1, 1, 1' else set BGC_NCFORMAT = '0, 0, 0' @@ -531,7 +541,7 @@ set INT_BROMOUV = '0, 2, 2' set INT_PHOSY = '4, 2, 2' set INT_NFIX = '0, 2, 2' set INT_DNIT = '0, 2, 2' -if ($BLOM_N_DEPOSITION == TRUE) then +if ("$BLOM_N_DEPOSITION" == TRUE) then set FLX_NDEP = '0, 2, 2' else set FLX_NDEP = '0, 0, 0' @@ -680,8 +690,8 @@ set BUR_SSSC12 = '0, 0, 2' set BUR_SSSTER = '0, 0, 2' # if partial coupling, enable SSS relaxation -if ($BLOM_COUPLING =~ *partial*) then - if ($BLOM_VCOORD == isopyc_bulkml) then +if ("$BLOM_COUPLING" =~ *partial*) then + if ("$BLOM_VCOORD" == isopyc_bulkml) then set SRXDAY = 6. else set SRXDAY = 60. @@ -692,17 +702,17 @@ if ($BLOM_COUPLING =~ *partial*) then endif # set grid dependent parameters -if ($OCN_GRID == gx1v5 || $OCN_GRID == gx1v6) then +if ("$OCN_GRID" == gx1v5 || "$OCN_GRID" == gx1v6) then set BACLIN = 1800. set BATROP = 36. -else if ($OCN_GRID == gx3v7) then +else if ("$OCN_GRID" == gx3v7) then set BACLIN = 3600. set BATROP = 72. -else if ($OCN_GRID == tnx2v1 ) then +else if ("$OCN_GRID" == tnx2v1 ) then set BACLIN = 4800. set BATROP = 96. set EGC = 0.5 - if ($BLOM_UNIT == cgs) then + if ("$BLOM_UNIT" == cgs) then set EGMXDF = 1000.e4 else set EGMXDF = 1000. @@ -712,23 +722,23 @@ else if ($OCN_GRID == tnx2v1 ) then set CWMI = " 53, 54" set CWMJ = " 137, 137" set CWMWTH = " 30.e3, 30.e3" -else if ($OCN_GRID == tnx1.5v1 ) then +else if ("$OCN_GRID" == tnx1.5v1 ) then set BACLIN = 4800. set BATROP = 96. set EGC = 0.5 - if ($BLOM_UNIT == cgs) then + if ("$BLOM_UNIT" == cgs) then set EGMXDF = 1000.e4 else set EGMXDF = 1000. endif -else if ($OCN_GRID == tnx1v1 || $OCN_GRID == tnx1v3 || $OCN_GRID == tnx1v4) then - if ($OCN_NCPL == 24) then +else if ("$OCN_GRID" == tnx1v1 || "$OCN_GRID" == tnx1v3 || "$OCN_GRID" == tnx1v4) then + if ("$OCN_NCPL" == 24) then set BACLIN = 3600. set BATROP = 60. set CWBDTS = .75e-4 set NIWGF = .4 set SMTFRC = .false. - if ($BLOM_VCOORD == isopyc_bulkml) then + if ("$BLOM_VCOORD" == isopyc_bulkml) then set CE = .5 endif else @@ -740,10 +750,10 @@ else if ($OCN_GRID == tnx1v1 || $OCN_GRID == tnx1v3 || $OCN_GRID == tnx1v4) then set CWMI = " 105, 106" set CWMJ = " 273, 273" set CWMWTH = " 30.e3, 30.e3" -else if ($OCN_GRID == tnx0.25v1 || $OCN_GRID == tnx0.25v3 || $OCN_GRID == tnx0.25v4) then +else if ("$OCN_GRID" == tnx0.25v1 || "$OCN_GRID" == tnx0.25v3 || "$OCN_GRID" == tnx0.25v4) then set BACLIN = 900. set BATROP = 15. - if ($BLOM_UNIT == cgs) then + if ("$BLOM_UNIT" == cgs) then set MDV2HI = .15 set MDV2LO = .15 set MDV4HI = 0. @@ -766,15 +776,15 @@ else if ($OCN_GRID == tnx0.25v1 || $OCN_GRID == tnx0.25v3 || $OCN_GRID == tnx0.2 set CWBDLS = 25. set EDWMTH = "'step'" set EGC = 0.85 - if ($BLOM_UNIT == cgs) then + if ("$BLOM_UNIT" == cgs) then set EGMXDF = 1500.e4 else set EGMXDF = 1500. endif - if ($BLOM_VCOORD == isopyc_bulkml) then + if ("$BLOM_VCOORD" == isopyc_bulkml) then set CE = 1.0 endif -else if ($OCN_GRID == tnx0.125v4) then +else if ("$OCN_GRID" == tnx0.125v4) then set BACLIN = 300. set BATROP = 6. set EGMNDF = 0. @@ -782,7 +792,7 @@ else if ($OCN_GRID == tnx0.125v4) then set EDWMTH = "'step'" set CWBDTS = .75e-4 set CWBDLS = 25 - if ($BLOM_UNIT == cgs) then + if ("$BLOM_UNIT" == cgs) then set MDV2HI = .1 set MDV2LO = .1 set MDV4HI = 0. @@ -803,7 +813,8 @@ else if ($OCN_GRID == tnx0.125v4) then set VSC4LO = .06 set LTEDTP = "'layer'" else - echo "$0 ERROR: Cannot deal with GRID = $OCN_GRID " + echo "OCN_GRID is $OCN_GRID \n" + echo "$0 ERROR: Cannot deal with GRID equal to $OCN_GRID " exit -1 endif @@ -814,7 +825,7 @@ set INIPO4 = "'$DIN_LOC_ROOT/ocn/blom/inicon/woa13_phosphate_OMIPinit_20171107.n set INIOXY = "'$DIN_LOC_ROOT/ocn/blom/inicon/woa13_oxygen_OMIPinit_20171107.nc'" set ININO3 = "'$DIN_LOC_ROOT/ocn/blom/inicon/woa13_nitrate_OMIPinit_20171107.nc'" set INISIL = "'$DIN_LOC_ROOT/ocn/blom/inicon/woa13_silicate_OMIPinit_20171107.nc'" -if ($HAMOCC_CISO == TRUE) then +if ("$HAMOCC_CISO" == TRUE) then set INID13C = "'$DIN_LOC_ROOT/ocn/blom/inicon/d13C_permil_20180609.nc'" set INID14C = "'$DIN_LOC_ROOT/ocn/blom/inicon/d14C_permil_20180609.nc'" else @@ -823,7 +834,7 @@ set INID14C = "''" endif # set grid dependent input files -if ($OCN_GRID == tnx2v1) then +if ("$OCN_GRID" == tnx2v1) then set GRFILE = "'$DIN_LOC_ROOT/ocn/blom/grid/grid_tnx2v1_20130206.nc'" set ICFILE = "'$DIN_LOC_ROOT/ocn/blom/inicon/inicon_tnx2v1_20130419.nc'" set TDFILE = "'$DIN_LOC_ROOT/ocn/blom/bndcon/tidal_dissipation_tnx2v1_20130419.nc'" @@ -834,17 +845,17 @@ if ($OCN_GRID == tnx2v1) then set FEDEPFILE = "'$DIN_LOC_ROOT/ocn/blom/bndcon/dustdep_mhw2006_tnx2v1_20130506.nc'" set SWACLIMFILE = "''" set SEDPORFILE = "''" - if ($BLOM_RIVER_NUTRIENTS == TRUE) then + if ("$BLOM_RIVER_NUTRIENTS" == TRUE) then set RIVINFILE = "'$DIN_LOC_ROOT/ocn/blom/bndcon/river_nutrients_GNEWS2000_tnx2v1_20170915.nc'" else set RIVINFILE = "''" endif - if ($BLOM_N_DEPOSITION == TRUE) then + if ("$BLOM_N_DEPOSITION" == TRUE) then set NDEPFILE = "'$DIN_LOC_ROOT/ocn/blom/bndcon/$NDEPFNAME'" else set NDEPFILE = "''" endif -else if ($OCN_GRID == tnx1v4) then +else if ("$OCN_GRID" == tnx1v4) then set GRFILE = "'$DIN_LOC_ROOT/ocn/blom/grid/grid_tnx1v4_20170622.nc'" set ICFILE = "'$DIN_LOC_ROOT/ocn/blom/inicon/inicon_tnx1v4_20170622.nc'" set TDFILE = "'$DIN_LOC_ROOT/ocn/blom/bndcon/tidal_dissipation_tnx1v4_20170605.nc'" @@ -855,22 +866,22 @@ else if ($OCN_GRID == tnx1v4) then set SCFILE = "'$DIN_LOC_ROOT/ocn/blom/bndcon/sss_clim_core_tnx1v4_20170604.nc'" set FEDEPFILE = "'$DIN_LOC_ROOT/ocn/blom/bndcon/dustdep_mhw2006_tnx1v4_20171107.nc'" set SEDPORFILE = "''" - if ($HAMOCC_VSLS == TRUE) then + if ("$HAMOCC_VSLS" == TRUE) then set SWACLIMFILE = "'$DIN_LOC_ROOT/ocn/blom/bndcon/Annual_clim_swa_tnx1v4_20210415.nc'" else set SWACLIMFILE = "''" endif - if ($BLOM_RIVER_NUTRIENTS == TRUE) then + if ("$BLOM_RIVER_NUTRIENTS" == TRUE) then set RIVINFILE = "'$DIN_LOC_ROOT/ocn/blom/bndcon/river_nutrients_GNEWS2000_tnx1v4_20170820.nc'" else set RIVINFILE = "''" endif - if ($BLOM_N_DEPOSITION == TRUE) then + if ("$BLOM_N_DEPOSITION" == TRUE) then set NDEPFILE = "'$DIN_LOC_ROOT/ocn/blom/bndcon/$NDEPFNAME'" else set NDEPFILE = "''" endif -else if ($OCN_GRID == tnx0.25v4) then +else if ("$OCN_GRID" == tnx0.25v4) then set GRFILE = "'$DIN_LOC_ROOT/ocn/blom/grid/grid_tnx0.25v4_20170622.nc'" set ICFILE = "'$DIN_LOC_ROOT/ocn/blom/inicon/inicon_tnx0.25v4_20170623.nc'" set TDFILE = "'$DIN_LOC_ROOT/ocn/blom/bndcon/tidal_dissipation_tnx0.25v4_20170626.nc'" @@ -882,17 +893,17 @@ else if ($OCN_GRID == tnx0.25v4) then set FEDEPFILE = "'$DIN_LOC_ROOT/ocn/blom/bndcon/dustdep_mhw2006_tnx0.25v4_20181004.nc'" set SWACLIMFILE = "''" set SEDPORFILE = "''" - if ($BLOM_RIVER_NUTRIENTS == TRUE) then + if ("$BLOM_RIVER_NUTRIENTS" == TRUE) then set RIVINFILE = "'$DIN_LOC_ROOT/ocn/blom/bndcon/river_nutrients_GNEWS2000_tnx0.25v4_20170821.nc'" else set RIVINFILE = "''" endif - if ($BLOM_N_DEPOSITION == TRUE) then + if ("$BLOM_N_DEPOSITION" == TRUE) then set NDEPFILE = "'$DIN_LOC_ROOT/ocn/blom/bndcon/$NDEPFNAME'" else set NDEPFILE = "''" endif -else if ($OCN_GRID == tnx0.125v4) then +else if ("$OCN_GRID" == tnx0.125v4) then set GRFILE = "'$DIN_LOC_ROOT/ocn/blom/grid/grid_tnx0.125v4_20221013.nc'" set ICFILE = "'$DIN_LOC_ROOT/ocn/blom/inicon/inicon_tnx0.125v4_20230318.nc'" set TDFILE = "'$DIN_LOC_ROOT/ocn/blom/bndcon/tidal_dissipation_tnx0.125v4_20221013.nc'" @@ -904,12 +915,12 @@ else if ($OCN_GRID == tnx0.125v4) then set FEDEPFILE = "'$DIN_LOC_ROOT/ocn/blom/bndcon/dustdep_mhw2006_tnx0.125v4_20221013.nc'" set SWACLIMFILE = "''" set SEDPORFILE = "''" - if ($BLOM_RIVER_NUTRIENTS == TRUE) then + if ("$BLOM_RIVER_NUTRIENTS" == TRUE) then set RIVINFILE = "'$DIN_LOC_ROOT/ocn/blom/bndcon/river_nutrients_GNEWS2000_tnx0.125v4_20221013.nc'" else set RIVINFILE = "''" endif - if ($BLOM_N_DEPOSITION == TRUE) then + if ("$BLOM_N_DEPOSITION" == TRUE) then set NDEPFILE = "'$DIN_LOC_ROOT/ocn/blom/bndcon/$NDEPFNAME'" else set NDEPFILE = "''" @@ -1098,7 +1109,7 @@ cat >! $RUNDIR/ocn_in$inststr << EOF / EOF -if ($BLOM_VCOORD == cntiso_hybrid) then +if ("$BLOM_VCOORD" == cntiso_hybrid) then cat >>! $RUNDIR/ocn_in$inststr << EOF &VCOORD @@ -1618,7 +1629,7 @@ cat >>! $RUNDIR/ocn_in$inststr << EOF / EOF -if ($ecosys == TRUE) then +if ("$ecosys" == TRUE) then cat >>! $RUNDIR/ocn_in$inststr << EOF ! NAMELIST FOR iHAMOCC OPTIONS diff --git a/cime_config/config_compsets.xml b/cime_config/config_compsets.xml index 96a73717..69fd3bce 100644 --- a/cime_config/config_compsets.xml +++ b/cime_config/config_compsets.xml @@ -4,9 +4,9 @@ ========================================= - compset naming convention + compset naming convention ========================================= - The compset longname below has the specified order + The compset longname below has the specified order atm, lnd, ice, ocn, river, glc wave cesm-options The notation for the compset longname is @@ -20,24 +20,33 @@ ROF = [RTM, SROF] GLC = [CISM1, CISM2, SGLC] WAV = [SWAV] - BGC = optional BGC scenario + BGC = optional BGC scenario The OPTIONAL %phys attributes specify submodes of the given system For example DOCN%DOM is the data ocean model for DOCN - ALL the possible %phys choices for each component are listed + ALL the possible %phys choices for each component are listed with the -list command for create_newcase - ALL data models must have a %phys option that corresponds to the data model mode + ALL data models must have a %phys option that corresponds to the data model mode Each compset node is associated with the following elements - - lname - - alias + - lname + - alias - support (optional description of the support level for this compset) Each compset node can also have the following attributes - grid (optional regular expression match for grid to work with the compset) - NOINY + NOINY_WW3 + 2000_DATM%NYF_SLND_CICE_BLOM_DROF%NYF_SGLC_WW3DEV + + + NOINYOC_WW3 + 2000_DATM%NYF_SLND_CICE_BLOM%ECO_DROF%NYF_SGLC_WW3DEV + + + + NOINY 2000_DATM%NYF_SLND_CICE_BLOM_DROF%NYF_SGLC_SWAV @@ -107,5 +116,3 @@ - - diff --git a/cime_config/testdefs/testlist_blom.xml b/cime_config/testdefs/testlist_blom.xml index b9222f55..5704bcc4 100644 --- a/cime_config/testdefs/testlist_blom.xml +++ b/cime_config/testdefs/testlist_blom.xml @@ -1,8 +1,23 @@ - + - + + + + + + + + + + + + + + + + From d2fe35b4c6b0c23990d43d106275a0fe2c57653b Mon Sep 17 00:00:00 2001 From: Mariana Vertenstein Date: Fri, 14 Jul 2023 14:40:08 +0200 Subject: [PATCH 2/6] added wavice user mods for testing --- .../testmods_dirs/blom/wavice/user_nl_cice | 18 ++++++++++++++++ .../testmods_dirs/blom/wavice/user_nl_cpl | 21 +++++++++++++++++++ 2 files changed, 39 insertions(+) create mode 100644 cime_config/testdefs/testmods_dirs/blom/wavice/user_nl_cice create mode 100644 cime_config/testdefs/testmods_dirs/blom/wavice/user_nl_cpl diff --git a/cime_config/testdefs/testmods_dirs/blom/wavice/user_nl_cice b/cime_config/testdefs/testmods_dirs/blom/wavice/user_nl_cice new file mode 100644 index 00000000..313b09e6 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/blom/wavice/user_nl_cice @@ -0,0 +1,18 @@ +!---------------------------------------------------------------------------------- +! Users should add all user specific namelist changes below in the form of +! namelist_var = new_namelist_value +! Note - that it does not matter what namelist group the namelist_var belongs to +!---------------------------------------------------------------------------------- + +tr_fsd = .true. +nfsd = 12 +wave_spec_type = "random" +histfreq = 'm','d','x','x','x' +histfreq_n = 1,1,0,0,0 +f_afsd = 'md' +f_dafsd_newi = 'md' +f_dafsd_weld = 'md' +!f_wave_sig_ht = 'md' +f_dafsd_latg = 'md' +f_dafsd_wave = 'md' +wave_spec_type = 'constant' \ No newline at end of file diff --git a/cime_config/testdefs/testmods_dirs/blom/wavice/user_nl_cpl b/cime_config/testdefs/testmods_dirs/blom/wavice/user_nl_cpl new file mode 100644 index 00000000..cece546c --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/blom/wavice/user_nl_cpl @@ -0,0 +1,21 @@ +!------------------------------------------------------------------------ +! Users should ONLY USE user_nl_cpl to change namelists variables +! for namelist variables in drv_in (except for the ones below) and +! any keyword/values in seq_maps.rc +! Users should add ALL user specific namelist and seq_maps.rc changes below +! using the following syntax +! namelist_var = new_namelist_value +! or +! mapname = new_map_name +! For example to change the default value of ocn2atm_fmapname to 'foo' use +! ocn2atm_fmapname = 'foo' +! +! Note that some namelist variables MAY NOT be changed in user_nl_cpl - +! they are defined in a $CASEROOT xml file and must be changed with +! xmlchange. +! +! For example, rather than set username to 'foo' in user_nl_cpl, call +! ./xmlchange USER=foo +!------------------------------------------------------------------------ + +wav_coupling_to_cice=.true. From ab9a98e8b360c0e4e459a5ce00a77c9748e22c90 Mon Sep 17 00:00:00 2001 From: Mariana Vertenstein Date: Tue, 25 Jul 2023 11:35:30 +0200 Subject: [PATCH 3/6] updates to add ocn_in.readme and remove from buildnml --- cime_config/buildnml | 592 ++++---------------------------------- cime_config/ocn_in.readme | 554 +++++++++++++++++++++++++++++++++++ 2 files changed, 606 insertions(+), 540 deletions(-) create mode 100644 cime_config/ocn_in.readme diff --git a/cime_config/buildnml b/cime_config/buildnml index e8c45153..caf1f533 100755 --- a/cime_config/buildnml +++ b/cime_config/buildnml @@ -66,7 +66,9 @@ set DAY0 = `echo $RUN_STARTDATE | cut -c9-10` # Set namelist variables #------------------------------------------------------------------------------ +#------------------------------ # set LIMITS defaults +#------------------------------ set NDAY1 = 0 set NDAY2 = 0 set IDATE = $YEAR0$MONTH0$DAY0 @@ -158,7 +160,9 @@ else set IOTYPE = 0 endif +#------------------------------ # set VCOORD defaults +#------------------------------ set VCOORD_TYPE = "'$BLOM_VCOORD'" set RECONSTRUCTION_METHOD = "'ppm'" set DENSITY_LIMITING = "'monotonic'" @@ -176,7 +180,9 @@ set DPMIN_INTERIOR = .1 set DKTZU = 4 set DKTZL = 1 +#------------------------------ # set DIFFUSION defaults +#------------------------------ set EITMTH = "'gm'" set EDRITP = "'large scale'" set EDWMTH = "'smooth'" @@ -219,7 +225,9 @@ else set LTEDTP = "'neutral'" endif +#------------------------------ # set BGCNML defaults +#------------------------------ set ATM_CO2 = "$CCSM_CO2_PPMV" if ("$BLOM_RIVER_NUTRIENTS" == TRUE) then set DO_RIVINPT = .true. @@ -291,7 +299,9 @@ set L_3DVARSEDPOR = .false. set SEDPORFILE = "''" +#------------------------------ # set DIAPHY defaults +#------------------------------ set GLB_FNAMETAG = "'hd','hm','hy'" set GLB_AVEPERIO = '1, 30, 365' if ("$TEST" == TRUE) then @@ -306,25 +316,37 @@ else set GLB_NCFORMAT = '0, 0, 0' endif set H2D_ABSWND = '0, 4, 0' + set H2D_ALB = '0, 0, 0' + set H2D_BTMSTR = '0, 4, 0' set H2D_BRNFLX = '0, 4, 0' set H2D_BRNPD = '0, 4, 0' + set H2D_DFL = '0, 0, 0' + set H2D_EVA = '0, 4, 0' set H2D_FICE = '0, 4, 0' set H2D_FMLTFZ = '0, 4, 0' + set H2D_HICE = '0, 0, 0' + set H2D_HMLTFZ = '0, 4, 0' + set H2D_HSNW = '0, 0, 0' set H2D_IAGE = '0, 0, 0' + set H2D_IDKEDT = '0, 4, 0' set H2D_LAMULT = '0, 4, 0' set H2D_LASL = '0, 4, 0' set H2D_LIP = '0, 4, 0' + set H2D_MAXMLD = '4, 4, 0' + set H2D_MLD = '0, 4, 0' + set H2D_MLTS = '4, 4, 0' + set H2D_MLTSMN = '0, 4, 0' set H2D_MLTSMX = '0, 4, 0' set H2D_MLTSSQ = '0, 4, 0' @@ -343,32 +365,46 @@ set H2D_RNFFLX = '0, 4, 0' set H2D_SALFLX = '0, 4, 0' set H2D_SALRLX = '0, 4, 0' set H2D_SBOT = '0, 4, 0' + set H2D_SEALV = '4, 4, 0' + set H2D_SLVSQ = '0, 4, 0' set H2D_SFL = '0, 4, 0' set H2D_SOP = '0, 4, 0' set H2D_SIGMX = '0, 4, 0' + set H2D_SSS = '4, 4, 0' set H2D_SSSSQ = '4, 4, 0' set H2D_SST = '4, 4, 0' set H2D_SSTSQ = '4, 4, 0' + set H2D_SURFLX = '0, 4, 0' set H2D_SURRLX = '0, 4, 0' set H2D_SWA = '0, 4, 0' + set H2D_T20D = '4, 4, 0' + set H2D_TAUX = '0, 4, 0' set H2D_TAUY = '0, 4, 0' set H2D_TBOT = '0, 4, 0' + set H2D_TICE = '0, 0, 0' set H2D_TSRF = '0, 0, 0' + set H2D_UB = '0, 4, 0' + set H2D_UICE = '0, 0, 0' + set H2D_USTAR = '0, 4, 0' set H2D_USTAR3 = '0, 4, 0' + set H2D_USTOKES = '0, 0, 0' + set H2D_VB = '0, 4, 0' + set H2D_VICE = '0, 0, 0' set H2D_VSTOKES = '0, 0, 0' + set H2D_ZTX = '0, 4, 0' set LYR_BFSQ = '0, 4, 0' set LYR_DIFDIA = '0, 4, 0' @@ -381,10 +417,13 @@ set LYR_DP = '0, 4, 0' set LYR_DZ = '0, 4, 0' set LYR_SALN = '0, 4, 0' set LYR_TEMP = '0, 4, 0' + set LYR_TRC = '0, 0, 0' + set LYR_UFLX = '0, 4, 0' set LYR_UTFLX = '0, 4, 0' set LYR_USFLX = '0, 4, 0' + set LYR_UMFLTD = '0, 0, 4' set LYR_UMFLSM = '0, 0, 4' set LYR_UTFLTD = '0, 0, 4' @@ -393,10 +432,12 @@ set LYR_UTFLLD = '0, 0, 4' set LYR_USFLTD = '0, 0, 4' set LYR_USFLSM = '0, 0, 4' set LYR_USFLLD = '0, 0, 4' + set LYR_UVEL = '0, 4, 0' set LYR_VFLX = '0, 4, 0' set LYR_VTFLX = '0, 4, 0' set LYR_VSFLX = '0, 4, 0' + set LYR_VMFLTD = '0, 0, 4' set LYR_VMFLSM = '0, 0, 4' set LYR_VTFLTD = '0, 0, 4' @@ -405,6 +446,7 @@ set LYR_VTFLLD = '0, 0, 4' set LYR_VSFLTD = '0, 0, 4' set LYR_VSFLSM = '0, 0, 4' set LYR_VSFLLD = '0, 0, 4' + set LYR_VVEL = '0, 4, 0' set LYR_WFLX = '0, 4, 0' set LYR_WFLX2 = '0, 4, 0' @@ -422,10 +464,13 @@ set LVL_DIFISO = '0, 4, 0' set LVL_DZ = '0, 4, 0' set LVL_SALN = '0, 4, 0' set LVL_TEMP = '0, 4, 0' + set LVL_TRC = '0, 0, 0' + set LVL_UFLX = '0, 4, 0' set LVL_UTFLX = '0, 4, 0' set LVL_USFLX = '0, 4, 0' + set LVL_UMFLTD = '0, 0, 4' set LVL_UMFLSM = '0, 0, 4' set LVL_UTFLTD = '0, 0, 4' @@ -434,10 +479,12 @@ set LVL_UTFLLD = '0, 0, 4' set LVL_USFLTD = '0, 0, 4' set LVL_USFLSM = '0, 0, 4' set LVL_USFLLD = '0, 0, 4' + set LVL_UVEL = '0, 4, 0' set LVL_VFLX = '0, 4, 0' set LVL_VTFLX = '0, 4, 0' set LVL_VSFLX = '0, 4, 0' + set LVL_VMFLTD = '0, 0, 4' set LVL_VMFLSM = '0, 0, 4' set LVL_VTFLTD = '0, 0, 4' @@ -446,6 +493,7 @@ set LVL_VTFLLD = '0, 0, 4' set LVL_VSFLTD = '0, 0, 4' set LVL_VSFLSM = '0, 0, 4' set LVL_VSFLLD = '0, 0, 4' + set LVL_VVEL = '0, 4, 0' set LVL_WFLX = '0, 4, 0' set LVL_WFLX2 = '0, 4, 0' @@ -475,7 +523,9 @@ set MSC_TEMPGA = '0, 4, 0' set MSC_SSSGA = '0, 4, 0' set MSC_SSTGA = '0, 4, 0' +#------------------------------ # set DIABGC defaults +#------------------------------ set BGC_FNAMETAG = "'hbgcd','hbgcm','hbgcy'" set BGC_AVEPERIO = '1,30,365' set BGC_FILEFREQ = '30,30,365' @@ -950,96 +1000,9 @@ foreach mem ("`seq $NINST_OCN`") endif end +cp ocn_in.readme $RUNDIR/. + cat >! $RUNDIR/ocn_in$inststr << EOF -! LIMITS NAMELIST -! -! CONTENTS: -! -! NDAY1 : First day of integration (i) -! NDAY2 : Last day of integration (i) -! IDATE : Model date in YYYYMMDD (i) -! IDATE0 : Initial experiment date in YYYYMMDD (i) -! RUNID : Experiment name (a) -! EXPCNF : Experiment configuration (a) -! RUNTYP : CESM run type (a) -! GRFILE : Name of file containing grid specification (a) -! ICFILE : Name of file containing initial conditions, that is either -! a valid restart file or 'inicon.nc' if climatological based -! initial conditions are desired (a) -! PREF : Reference pressure for potential density (g/cm/s2) (f) -! BACLIN : Baroclinic time step (sec) (f) -! BATROP : Barotropic time step (sec) (f) -! MDV2HI : Laplacian diffusion velocity for momentum dissipation (cm/s) (f) -! MDV2LO : Laplacian diffusion velocity for momentum dissipation (cm/s) (f) -! MDV4HI : Biharmonic diffusion velocity for momentum dissipation (cm/s) (f) -! MDV4LO : Biharmonic diffusion velocity for momentum dissipation (cm/s) (f) -! MDC2HI : Laplacian diffusivity for momentum dissipation (cm**2/s) (f) -! MDC2LO : Laplacian diffusivity for momentum dissipation (cm**2/s) (f) -! VSC2HI : Parameter in deformation-dependent Laplacian viscosity (f) -! VSC2LO : Parameter in deformation-dependent Laplacian viscosity (f) -! VSC4HI : Parameter in deformation-dependent Biharmonic viscosity (f) -! VSC4LO : Parameter in deformation-dependent Biharmonic viscosity (f) -! CBAR : rms flow speed for linear bottom friction law (cm/s) (f) -! CB : Nondiemnsional coefficient of quadratic bottom friction (f) -! CWBDTS : Coastal wave breaking damping resiprocal time scale (1/s) (f) -! CWBDLS : Coastal wave breaking damping length scale (m) (f) -! MOMMTH : Momentum equation discretization method. Valid methods: -! 'enscon' (Sadourny (1975) enstrophy conserving), 'enecon' -! (Sadourny (1975) energy conserving), 'enedis' (Sadourny -! (1975) energy conserving with some dissipation) (a) -! BMCMTH : Baroclinic mass flux correction method. Valid methods: -! 'uc' (upstream column), 'dluc' (depth limited upstream -! column) (a) -! RMPMTH : Method of applying eddy-induced transport in the remap -! transport algorithm. Valid methods: 'eitvel', 'eitflx' (a) -! MLRTTP : Type of mixed layer restratification time scale. Valid -! types: 'variable', 'constant', 'limited' (a) -! RM0 : Efficiency factor of wind TKE generation in the Oberhuber -! (1993) TKE closure () (f) -! RM5 : Efficiency factor of TKE generation by momentum -! entrainment in the Oberhuber (1993) TKE closure () (f) -! CE : Efficiency factor for the restratification by mixed layer -! eddies (Fox-Kemper et al., 2008) () (f) -! TDFILE : Name of file containing tidal wave energy dissipation -! divided by by bottom buoyancy frequency (a) -! NIWGF : Global factor applied to the energy input by near-intertial -! motions () (f) -! NIWBF : Fraction of near-inertial energy dissipated in the boundary -! layer () (f) -! NIWLF : Fraction of near-inertial energy dissipated locally beneath -! the boundary layer () (f) -! SWAMTH : Shortwave radiation absorption method. Valid methods: -! 'top-layer', 'jerlov', 'chlorophyll' (a) -! JWTYPE : Number indicating the Jerlov (1968) water type (i) -! CHLOPT : Chlorophyll concentration option. Valid options: -! 'climatology' (a) -! CCFILE : Name of file containing chlorophyll concentration climatology (a) -! TRXDAY : e-folding time scale (days) for SST relax., if 0 no relax. (f) -! SRXDAY : e-folding time scale (days) for SSS relax., if 0 no relax. (f) -! TRXDPT : Maximum mixed layer depth for e-folding SST relaxation (m) (f) -! SRXDPT : Maximum mixed layer depth for e-folding SSS relaxation (m) (f) -! TRXLIM : Max. absolute value of SST difference in relaxation (degC) (f) -! SRXLIM : Max. absolute value of SSS difference in relaxation (psu) (f) -! APTFLX : Apply diagnosed heat flux flag (l) -! APSFLX : Apply diagnosed freshwater flux flag (l) -! DITFLX : Diagnose heat flux flag (l) -! DISFLX : Diagnose freshwater flux flag (l) -! SRXBAL : Balance the SSS relaxation (l) -! SCFILE : Name of file containing SSS climatology used for relaxation (a) -! WAVSRC : Source of wave fields. Valid source: 'none', 'param', 'extern' (a) -! SMTFRC : Smooth CESM forcing (l) -! SPRFAC : Send precipitation/runoff factor to CESM coupler (l) -! ATM_PATH : Path to forcing fields in case of EXPCNF 'ben02clim' or -! 'ben02syn' (a) -! ITEST : Global i-index of point diagnostics (i) -! JTEST : Global j-index of point diagnostics (i) -! CNSVDI : Conservation diagnostics flag (l) -! CSDIAG : Checksum diagnostics flag (l) -! RSTFRQ : Restart frequency in days (30=1month,365=1year) (i) -! RSTFMT : Format of restart file (valid arguments are 0 for classic, -! 1 for 64-bit offset and 2 for netcdf4/hdf5 format) (i) -! RSTCMP : Compression flag for restart file (i) -! IOTYPE : 0 = netcdf, 1 = pnetcdf &LIMITS NDAY1 = $NDAY1 NDAY2 = $NDAY2 @@ -1135,55 +1098,6 @@ endif cat >>! $RUNDIR/ocn_in$inststr << EOF -! NAMELIST FOR DIFFUSION PARAMETERS -! -! CONTENTS: -! -! EITMTH : Eddy-induced transport parameterization method. Valid -! methods: 'intdif', 'gm' (a) -! EDRITP : Type of Richardson number used in eddy diffusivity -! computation. Valid types: 'shear', 'large scale' (a) -! EDWMTH : Method to estimate eddy diffusivity weight as a function of -! the ration of Rossby radius of deformation to the -! horizontal grid spacing. Valid methods: 'smooth', 'step' (a) -! MLRTTP : Type of mixed layer restratification time scale. Valid -! types: 'variable', 'constant', 'limited' (a) -! EDDF2D : If true, eddy diffusivity has a 2d structure (l) -! EDSPRS : Apply eddy mixing suppression away from steering level (l) -! EGC : Parameter c in Eden and Greatbatch (2008) parameterization (f) -! EGGAM : Parameter gamma in E. & G. (2008) param. (f) -! EGLSMN : Minimum eddy length scale in E. & G. (2008) param. (cm) (f) -! EGMNDF : Minimum diffusivity in E. & G. (2008) param. (cm**2/s) (f) -! EGMXDF : Maximum diffusivity in E. & G. (2008) param. (cm**2/s) (f) -! EGIDFQ : Factor relating the isopycnal diffusivity to the layer -! interface diffusivity in the Eden and Greatbatch (2008) -! parameterization. egidfq=difint/difiso () (f) -! TBFILE : Name of file containing topographic beta parameter (a) -! RHISCF : Linear scaling parameter for topographic rhines scale () (f) -! EDANIS : If true, apply anisotropy correction to eddy diffusivity (l) -! REDI3D : If true, then isopycnal/neutral diffusion will have 3D -! structure based in the 3D structure of anisotropy (l) -! RHSCTP : If true, use the minimum of planetary and topographic beta -! to define the Rhines scale (l) -! RI0 : Critical gradient richardson number for shear driven -! vertical mixing () (f) -! BDMTYP : Type of background diapycnal mixing. If bdmtyp=1 the -! background diffusivity is a constant divided by the -! Brunt-Vaisala frequency, if bdmtyp=2 the background -! diffusivity is constant () (i) -! BDMC1 : Background diapycnal diffusivity times buoyancy frequency -! frequency (cm**2/s**2) (f) -! BDMC2 : Background diapycnal diffusivity (cm**2/s) (f) -! BDMLDP : Make the background mixing latitude dependent according to -! Gregg et al. (2003) (l) -! TKEPF : Fraction of surface TKE that penetrates beneath mixed layer -! () (f) -! SMOBLD : If true, apply lateral smoothing of CVMix estimated -! boundary layer depth (l) -! LNGMTP : Type of CVMix Langmuir turbulence parameterization. Valid -! types: 'none', 'vr12-ma', 'lf17' -! LTEDTP : Type of lateral tracer eddy diffusion: Valid methods: -! 'layer', 'neutral'. &DIFFUSION EITMTH = $EITMTH EDRITP = $EDRITP @@ -1216,17 +1130,6 @@ EOF if ($?CWMTAG) then cat >>! $RUNDIR/ocn_in$inststr << EOF -! NAMELIST FOR CHANNEL WIDTH MODIFICATIONS -! -! CONTENTS: -! -! CWMTAG : Array of geographical names of channels to be modified (a) -! CWMEDG : Array of C grid cell edges to be modified. Valid options: -! 'u' or 'v' (a) -! CWMI : Array of grid cell i-indices (i) -! CWMJ : Array of grid cell j-indices (i) -! CWMWTH : Array of modified grid cell widths (m) (f) -! &CWMOD CWMTAG = $CWMTAG CWMEDG = $CWMEDG @@ -1239,20 +1142,6 @@ endif cat >>! $RUNDIR/ocn_in$inststr << EOF -! NAMELIST FOR MERIDIONAL OVERTURNING AND FLUX DIAGNOSTICS -! -! CONTENTS: -! -! MER_ORFILE : Name of file containing ocean region specification (a) -! MER_MIFILE : Name of file containing zonal section specification for -! meridional transport computation (a) -! MER_REGNAM : Array of region names for meridional overturning and flux -! diagnostics (a) -! MER_REGFLG : Array of mask flags in ocean regions file to be included -! for each region (i) -! MER_MINLAT : Minimum latitude to be considered for each region (f) -! MER_MAXLAT : Maximum latitude to be considered for each region (f) -! &MERDIA MER_ORFILE = $MER_ORFILE MER_MIFILE = $MER_MIFILE @@ -1265,192 +1154,10 @@ cat >>! $RUNDIR/ocn_in$inststr << EOF MER_MAXLAT = 90., 90., 90., 90. / -! NAMELIST FOR SECTION TRANSPORT DIAGNOSTICS -! -! CONTENTS: -! -! SEC_SIFILE : Name of file containing section specification for section -! transport computation (a) -! &SECDIA SEC_SIFILE = $SEC_SIFILE / -! IO-NAMELIST FOR DIAGNOSTIC OUTPUT -! -! Description: -! BLOM supports multiple output groups for its diagnostic output. -! Each output group is represented by one column in the namlist and may -! have its own output format, averaging period, and file frequency. -! The maximum number of output groups is currently limited to 10 but -! can be changed easily in mod_dia.F. -! -! The output precision can be choosen on a per-variable basis. -! -! Multiple time-slices can be written to the same output file -! provided that no variable is written in packed data format -! (i.e. as int2 with scale factor and offset). -! -! Compression of the output (i.e. storage of only wet points) -! and the file format can be choosen on a per-file basis. -! -! All time periods are specified in number of days for positive -! integer values and fraction of day for negative integer values. -! The length of the actual calendar month is used if 30 is written. -! The length of the actual calendar year is used if 365 is written. -! A variable is not written when 0 is specified. -! -! Namelist acronyms: -! GLB_ - global parameters i.e. valid for entire output group -! H2D_ - 2d fields with the horizontal dimensions -! LYR_ - 3d fields with sigma layers as vertical coordinate -! LVL_ - 3d fields with levitus leves as vertical coordinate -! MSC_ - miscellanous, non-gridded fields -! -! Global parameters: -! FNAMETAG - tag used in file name (c10) -! AVEPERIO - average period in days (i) -! FILEFREQ - how often to start a new file in days (i) -! COMPFLAG - switch for compressed/uncompressed output (i) -! NCFORMAT - netcdf format (valid arguments are 0 for classic, -! 1 for 64-bit offset and 2 for netcdf4/hdf5 format) -! -! Arguments for diagnostic variables: -! 0 - variable is not written -! 2 - variable is written as int2 with scale factor and offset -! 4 - variable is written as real4 -! 8 - variable is written as real8 -! -! Output variables: -! ABSWND - absolute wind speed [m s-1] -! ALB - surface albedo [] -! BTMSTR - Barotropic mass streamfunction [kg s-1] -! BRNFLX - brine flux [kg m-2 s-1] -! BRNPD - brine plume depth [m] -! DFL - non-solar heat flux derivative [W m-2 K-1] -! EVA - evaporation [kg m-2 s-1] -! FICE - ice concentration [%] -! FMLTFZ - fresh water flux due to melting/freezing [kg m-2 s-1] -! HICE - ice thickness [m] -! HMLTFZ - heat flux due to melting/freezing [W m-2] -! HSNW - snow depth [m] -! IAGE - ice age [d] -! IDKEDT - mixed layer inertial kinetic energy tendency [kg s-3] -! LAMULT - Langmuir enhancement factor [] -! LASL - Surface layer averaged Langmuir number [] -! LIP - liquid precipitation [kg m-2 s-1] -! MAXMLD - maximum mixed layer depth [m] -! MLD - mixed layer depth [m] -! MLTS - mixed layer thickness using "sigma-t" criterion [m] -! MLTSMN - minimum mixed layer thickness using "sigma-t" criterion [m] -! MLTSMX - maximum mixed layer thickness using "sigma-t" criterion [m] -! MLTSSQ - mixed layer thickness squared using "sigma-t" criterion [m2] -! MTKEUS - mixed layer TKE tendency related to friction velocity [kg s-3] -! MTKENI - mixed layer TKE tendency related to near inertial mot. [kg s-3] -! MTKEBF - mixed layer TKE tendency related to buoyancy forcing [kg s-3] -! MTKERS - mixed layer TKE tendency related to eddy restrat. [kg s-3] -! MTKEPE - mixed layer TKE tendency related to pot. energy change [kg s-3] -! MTKEKE - mixed layer TKE tendency related to kin. energy change [kg s-3] -! MTY - wind stress y-component [N m-2] -! NSF - non-solar heat flux [W m-2] -! PBOT - bottom pressure [Pa] -! PSRF - surface pressure [Pa] -! RFIFLX - frozen runoff [kg m-2 s-1] -! RNFFLX - liquid runoff [kg m-2 s-1] -! SALFLX - salt flux received by ocean [kg m-2 s-1] -! SALRLX - restoring salt flux received by ocean [kg m-2 s-1] -! SBOT - bottom salinity [g kg-1] -! SEALV - sea level [m] -! SLVSQ - sea level squared [m2] -! SFL - salt flux [kg m-2 s-1] -! SOP - solid precipitation [kg m-2 s-1] -! SIGMX - mixed layer density [kg m-3] -! SSS - ocean surface salinity [g kg-1] -! SSSSQ - ocean surface salinity squared [g2 kg-2] -! SST - ocean surface temperature [degC] -! SSTSQ - ocean surface temperature squared [degC2] -! SURFLX - heat flux received by ocean [W m-2] -! SURRLX - restoring heat flux received by ocean [W m-2] -! SWA - short-wave heat flux [W m-2] -! T20D - 20C isoterm depth [m] -! TAUX - momentum flux received by ocean x-component [N m-2] -! TAUY - momentum flux received by ocean y-component [N m-2] -! TBOT - bottom temperature [degC] -! TICE - ice temperature [degC] -! TSRF - surface temperature [degC] -! UB - barotropic velocity x-component [m s-1] -! UICE - ice velocity x-component [m s-1] -! USTAR - friction velocity [m s-1] -! USTAR3 - friction velocity cubed [m3 s-3] -! USTOKES - surface Stokes drift x-componen [m s-1] -! VB - barotropic velocity y-component [m s-1] -! VICE - ice velocity y-component [m s-1] -! VSTOKES - surface Stokes drift y-componen [m s-1] -! ZTX - wind stress x-component [N m-2] -! BFSQ - buoyancy frequency squared [s-1] -! DIFDIA - vertical diffusivity [log10(m2 s-1)|m2 s-1] -! DIFVMO - vertical momentum diffusivity [log10(m2 s-1)|m2 s-1] -! DIFVHO - vertical heat diffusivity [log10(m2 s-1)|m2 s-1] -! DIFVSO - vertical salt diffusivity [log10(m2 s-1)|m2 s-1] -! DIFINT - layer interface diffusivity [log10(m2 s-1)] -! DIFISO - isopycnal diffusivity [log10(m2 s-1)] -! DP - layer pressure thickness [Pa] -! DZ - layer thickness [m] -! SALN - salinity [g kg-1] -! TEMP - temperature [degC] -! TRC - tracer [] -! UFLX - mass flux in x-direction [kg s-1] -! UTFLX - heat flux in x-direction [W] -! USFLX - salt flux in x-direction [kg s-1] -! UMFLTD - mass flux due to thickness diffusion in x-direction [kg s-1] -! UMFLSM - mass flux due to submesoscale transport in x-direction [kg s-1] -! UTFLTD - heat flux due to thickness diffusion in x-direction [W] -! UTFLSM - heat flux due to submesoscale transport in x-direction [W] -! UTFLLD - heat flux due to lateral diffusion in x-direction [W] -! USFLTD - salt flux due to thickness diffusion in x-direction [kg s-1] -! USFLSM - salt flux due to submesoscale transport in x-direction [kg s-1] -! USFLLD - salt flux due to lateral diffusion in x-direction [kg s-1] -! UVEL - velocity x-component [m s-1] -! VFLX - mass flux in y-direction [kg s-1] -! VTFLX - heat flux in y-direction [W] -! VSFLX - salt flux in y-direction [kg s-1] -! VMFLTD - mass flux due to thickness diffusion in y-direction [kg s-1] -! VMFLSM - mass flux due to submesoscale transport in y-direction [kg s-1] -! VTFLTD - heat flux due to thickness diffusion in y-direction [W] -! VTFLSM - heat flux due to submesoscale transport in y-direction [W] -! VTFLLD - heat flux due to lateral diffusion in y-direction [W] -! VSFLTD - salt flux due to thickness diffusion in y-direction [kg s-1] -! VSFLSM - salt flux due to submesoscale transport in y-direction [kg s-1] -! VSFLLD - salt flux due to lateral diffusion in y-direction [kg s-1] -! VVEL - velocity x-component [m s-1] -! WFLX - vertical mass flux [kg s-1] -! WFLX2 - vertical mass flux squared [kg2 s-2] -! PV - potential vorticity [m-1 s-1] -! TKE - turbulent kinetic energy [m2 s-2] -! GLS_PSI - generic length scale [m2 s-3] -! IDLAGE - ideal age [year] -! MMFLXL - meridional overturning circ. (MOC) on isopycnic layers [kg s-1] -! MMFLXD - MOC on z-levels [kg s-1] -! MMFTDL - MOC due to thickness diffusion on isopycnic layers [kg s-1] -! MMFSML - MOC due to submesoscale transport on isopycnic layers [kg s-1] -! MMFTDD - MOC due to thickness diffusion on z-levels [kg s-1] -! MMFSMD - MOC due to submesoscale transport on z-levels [kg s-1] -! MHFLX - meridional heat flux [W] -! MHFTD - meridional heat flux due to thickness diffusion [W] -! MHFSM - meridional heat flux due to submesoscale transport [W] -! MHFLD - meridional heat flux due to lateral diffusion [W] -! MSFLX - meridional salt flux [kg s-1] -! MSFTD - meridional salt flux due to thickness diffusion [kg s-1] -! MSFSM - meridional salt flux due to submesoscale transport [kg s-1] -! MSFLD - meridional salt flux due to lateral diffusion [kg s-1] -! VOLTR - section transports [kg s-1] -! MASSGS - global sum of mass [kg] -! VOLGS - global sum of volume [m3] -! SALNGA - global average temperature [degC] -! TEMPGA - global average temperature [degC] -! SSSGA - global average sea surface salinity [g kg-1] -! SSTGA - global average sea surface temperature [degC] -! &DIAPHY GLB_FNAMETAG = $GLB_FNAMETAG GLB_AVEPERIO = $GLB_AVEPERIO @@ -1632,28 +1339,6 @@ EOF if ("$ecosys" == TRUE) then cat >>! $RUNDIR/ocn_in$inststr << EOF -! NAMELIST FOR iHAMOCC OPTIONS -! -! CONTENTS: -! -! ATM_CO2 : Atmospheric CO2 concentration [ppmv] -! FEDEPFILE : File name (incl. full path) for iron (dust) deposition data -! SWACLIMFILE : File name (incl. full path) for swa climatology field (needed -! if bromoform scheme is activated) -! DO_RIVINPT : Logical switch to activate riverine input -! RIVINFILE : File name (incl. full path) for riverine input data -! DO_NDEP : Logical switch to activate N-deposition -! NDEPFILE : File name (incl. full path) for atmopheric N-deposition data -! DO_SEDSPINUP: Logical switch to activate sediment spin-up -! SEDSPIN_YR_S: Start year for sediment spinup -! SEDSPIN_YR_E: End year for sediment spinup -! SEDSPIN_NCYC: Number of subcyles per time-step for sediment spinup -! INIXXX : Initial condition file for iHAMOCC, where XXX=DIC, ALK, PO4, -! OXY, NO3, SIL, D13C, and D14C -! WITH_DMSPH : Logical switch to activate DMS calculation as function of pH -! PI_PH_FILE : File name (incl. full path) for surface PI pH input data. -! L_3DVARSEDPOR : Logical switch to enable lon-lat-depth variable sediment porosity (as opposed to default: only depth) -! SEDPORFILE : File name (incl. full path) for sediment porosity &BGCNML ATM_CO2 = $CCSM_CO2_PPMV FEDEPFILE = $FEDEPFILE @@ -1681,17 +1366,6 @@ cat >>! $RUNDIR/ocn_in$inststr << EOF SEDPORFILE = $SEDPORFILE / -! NAMELIST FOR ALKALINIZATION SCENARIO -! -! CONTENTS: -! -! OALKSCEN : Name of alkalinization scenario ('const', 'ramp', or 'file') -! OALKFILE : Full path of the input file for the alkalinization scenario 'file' -! ADDALK : Pmol alkalinity/yr added in 'const' or 'ramp' scenarios -! CDRMIP_LATMAX : Max latitude where alkalinity is added in 'const' or 'ramp' scenarios -! CDRMIP_LATMIN : Min latitude where alkalinity is added in 'const' or 'ramp' scenarios -! RAMP_START : Start year for ramp up in 'ramp' scenario -! RAMP_END : End year for ramp up in 'ramp' scenario &BGCOAFX OALKSCEN = $BGCOAFX_OALKSCEN OALKFILE = $BGCOAFX_OALKFILE @@ -1702,168 +1376,6 @@ cat >>! $RUNDIR/ocn_in$inststr << EOF RAMP_END = $BGCOAFX_RAMP_END / -! IO-NAMELIST FOR DIAGNOSTIC iHAMOCC OUTPUT -! -! Namelist acronyms: -! GLB_ - global parameters i.e. valid for entire output group -! SRF_ - surface variables (includes some non-surface 2d fields) -! FLX_ - interior ocean particle fuxes at different depth (2d) -! INT_ - vertically integrated fields (2d) -! LYR_ - 3d fields with sigma layers as vertical coordinate -! LVL_ - 3d fields with levitus levels as vertical coordinate -! SDM_ - 3d sediment fields -! BUR_ - 2d fields of sediment burial -! -! Global parameters: -! FNAMETAG - tag used in file name (c10) -! AVEPERIO - average period in days (i) -! FILEFREQ - how often to start a new file in days (i) -! COMPFLAG - switch for compressed/uncompressed output (i) -! NCFORMAT - netcdf format (valid arguments are 0 for classic, -! 1 for 64-bit offset and 2 for netcdf4/hdf5 format) -! INVENTORY- how often to write an inventory of tracers to ocean -! output file: -! 0 : no output -! 1 : write inventory to standard output (log file) -! 2 : write output to inventory netCDF file -! -! Arguments for diagnostic variables: -! 0 - variable is not written -! 2 - variable is written as int2 with scale factor and offset -! 4 - variable is written as real4 -! 8 - variable is written as real8 -! -! Output variables: -! -! Main BGC tracer fields (SFR, LYR or LVL) -! DIC - Dissolved carbon (dissic) [mol C m-3] -! ALKALI - Alkalinity (talk) [eq m-3] -! OXYGEN - Oxygen (o2) [mol O2 m-3] -! ANO3 - Nitrate (no3) [mol N m-3] -! PHOSPH - Phosphorus (po4) [mol P m-3] -! IRON - Dissolved iron (dfe) [mol Fe m-3] -! SILICA - Silicate (si) [mol Si m-3] -! PHYTO - Phytoplankton (phyc) [mol C m-3] -! PH - pH (ph) [-log10([h+])] -! NATDIC - Natural dissolved carbon (natdissic) [mol C m-3] -! NATALKALI - Natural alkalinity (nattalk) [eq m-3] -! NATPH - Natural pH (natph) [-log10([h+])] -! -! Other 3d tracer or diagnostic variables (LYR or LVL) -! DP - Layer thickness (pddpo) [m] -! PREFO2 - preformed oxygen (p_o2) [mol O2 m-3] -! O2SAT - Saturated oxygen (satoxy) [mol O2 m-3] -! PREFPO4 - preformed phosphate (p_po4) [mol PO4 m-3] -! PREFALK - preformed alkalinity (p_talk) [eq m-3] -! PREFDIC - preformed DIC (p_dic) [mol C m-3] -! DICSAT - saturated DIC (dic_sat) [mol C m-3] -! POC - Detrius (detoc) [mol C m-3] -! CALC - CaCO3 shells (calc) [mol C m-3] -! OPAL - Opal shells (opal) [mol Si m-3] -! DOC - Dissolved organic carbon (dissoc) [mol C m-3] -! GRAZER - Zooplankton (zooc) [mol C m-3] -! PHOSY - Primary production (pp) [mol C m-3 s-1] -! CO3 - Carbonate ions (co3) [mol C m-3] -! N2O - Nitrous oxide concentration [mol N2O m-3] -! OMEGAA - Aragonite saturation state (omegaa) [1] -! OMEGAC - Calcite saturation state (omegac) [1] -! NATDIC - Natural dissolved carbon (natdissic) [mol C m-3] -! NATALKALI - Natural alkalinity (nattalk) [eq m-3] -! NATCO3 - Natural carbonate ion concentration (natco3) [mol C m-3] -! NATCALC - Natural CaCO3 shells (natcalc) [mol C m-3] -! NATOMEGAA - Natural aragonite saturation state (natomegaa) [1] -! NATOMEGAC - Natural calcite saturation state (natomegac) [1] -! DIC13 - Dissolved C13 (dissic13) [mol C m-3] -! DIC14 - Dissolved C14 (dissic14) [mol C m-3] -! D13C - delta 13C of DIC [1] -! D14C - delta 14C of DIC [1] -! BIGD14C - Delta 14C of DIC [1] -! POC13 - Particulate organic carbon 13 (detoc13) [mol C m-3] -! DOC13 - Dissolved organic carbon 13 (dissoc13) [mol C m-3] -! CALC13 - Particulate inorganic carbon 13 (calc13) [mol C m-3] -! PHYTO13 - 13C of phytoplankton biomass (phyc13) [mol C m-3] -! GRAZER13 - 13C of zootoplankton biomass (zooc13) [mol C m-3] -! CFC11 - CFC11 concentration [mol CFC11 m-3] -! CFC12 - CFC12 concentration [mol CFC12 m-3] -! SF6 - SF6 concentration [mol SF6 m-3] -! NOS - Number of sinking particles (aggregate scheme, nos) [cm-3] -! WPHY - Mass sinking velocity (aggregate scheme) [m d-1] -! WNOS - Number sinking velocity (aggregate scheme) [m d-1] -! EPS - Epsilon exponent (aggregate scheme) [1] -! ASIZE - Average particle size (aggregate scheme) -! -! 2d-fields (SFR) -! EXPORT - Export production (epc100) [mol C m-2 s-1] -! EXPOCA - Ca export production (epcalc100) [mol Ca m-2 s-1] -! EXPOSI - Si export production (epsi100) [mol Si m-2 s-1] -! PCO2 - Surface PCO2 (spco2) [uatm] -! PCO2M - Surface PCO2 under moist air assumption [uatm] -! KWCO2 - Piston velocity (kwco2) [m s-1] -! KWCO2KHM - Piston velocity times solubility (kwco2*kh; moist air) [m s-1 mol kg-1 uatm-1] -! CO2KH - CO2 solubility under dry air assumption (khd) [mol kg-1 atm-1] -! CO2KHM - CO2 solubility under moist air assumption (kh) [mol kg-1 atm-1] -! CO2FXD - Downward CO2 flux (co2fxd) [kg C m-2 s-1] -! CO2FXU - Upward CO2 flux (co2fxu) [kg C m-2 s-1] -! NIFLUX - Nitrogen flux (fgn2) [mol N2 m-2 s-1] -! OXFLUX - Oxygen flux (fgo2) [mol O2 m-2 s-1] -! N2OFX - Nitrous oxide flux [mol N2O m-2 s-1] -! DMSFLUX - DMS flux (dmsflux) [mol DMS m-2 s-1] -! DMS - surface DMS concentration (dms) [mol DMS m-3] -! DMSPROD - DMS production (dmsprod) [mol DMS m-2 s-1] -! DMS_BAC - DMS bacterial consuption (dms_bac) [mol DMS m-2 s-1] -! DMS_UV - DMS decomposition by UV (dms_uv) [mol DMS m-2 s-1] -! ATMCO2 - Atmospheric CO2 (atmco2) [ppm] -! ATMO2 - Atmospheric O2 (atmo2) [ppm] -! ATMN2 - Atmospheric N2 (atmn2) [ppm] -! NATPCO2 - Natural surface PCO2 (spco2) [uatm] -! NATCO2FX - Natural net CO2 flux (natco2fx) [kg C m-2 s-1] -! CO213FXD - Downward 13CO2 flux (co213fxd) [kg C m-2 s-1] -! CO213FXU - Upward 13CO2 flux (co213fxu) [kg C m-2 s-1] -! CO214FXD - Downward 14CO2 flux (co214fxd) [kg C m-2 s-1] -! CO214FXU - Upward 14CO2 flux (co214fxu) [kg C m-2 s-1] -! CFC11 - CFC11 flux [mol CFC11 m-2 s-1] -! CFC12 - CFC12 flux [mol CFC12 m-2 s-1] -! SF6 - SF6 flux [mol SF6 m-2 s-1] -! -! Vertically integrated fields (INT) -! PHOSY - Vertically integrated primary production [mol C m-3 s-1] -! NFIX - Vertically integrated nitrogen fixation -! DNIT - Vertically integrated denitrification -! -! Particle fluxes (FLX, e.g CARFLX****, where ****=0100,0500,1000,2000,4000, or _BOT), -! diffusive fluxes at the sediment - water-column interface (SEDIFF*), and other fluxes -! NDEP - Nitrogen deposition flux [mol N m-2 s-1] -! OALK - Flux of alkalinity due to ocean alkalinization [mol N m-2 s-1] -! CARFLX**** - POC flux at **** metres depth [mol C m-2 s-1] -! BSIFLX**** - Biogenic silica flux at **** metres depth [mol Si m-2 s-1] -! CALFLX**** - Calcium carbonate flux at **** metres depth [mol C m-2 s-1] -! SEDIFFIC - sediment - water-column diffusive flux of DIC [mol C m-2 s-1] -! SEDIFFAL - sediment - water-column diffusive flux of alkalinity [mol m-2 s-1] -! SEDIFFPH - sediment - water-column diffusive flux of phosphate [mol PO3 m-2 s-1] -! SEDIFFOX - sediment - water-column diffusive flux of oxygen [mol O2 m-2 s-1] -! SEDIFFN2 - sediment - water-column diffusive flux of N2 [mol N2 m-2 s-1] -! SEDIFFNO3 - sediment - water-column diffusive flux of nitrate [mol NO3 m-2 s-1] -! SEDIFFSI - sediment - water-column diffusive flux of silica [mol Si m-2 s-1] -! -! Sediment fields (SDM) -! POWAIC - (powdic) [mol C m-3] -! POWAAL - (powalk) [eq m-3] -! POWAPH - (powpho) [eq m-3] -! POWAOX - (powox) [mol O2 m-3] -! POWN2 - (pown2) [mol N2 m-3] -! POWNO3 - (powno3)[mol N m-3] -! POWASI - (powsi) [mol Si m-3] -! SSSO12 - (ssso12) [mol m-3] -! SSSSIL - (ssssil) [mol Si m-3] -! SSSC12 - (sssc12) [mol C m-3] -! SSSTER - (ssster) [mol m-3] -! -! Burial fields (BUR) -! SSSO12 - Solid sediment organic carbon [mol P m-2] -! SSSSIL - Solid sediment silica [mol Si m-2] -! SSSC12 - Solid sediment inorganic carbon [mol C m-2] -! SSSTER - -! &DIABGC GLB_FNAMETAG = $BGC_FNAMETAG GLB_AVEPERIO = $BGC_AVEPERIO diff --git a/cime_config/ocn_in.readme b/cime_config/ocn_in.readme new file mode 100644 index 00000000..8750f450 --- /dev/null +++ b/cime_config/ocn_in.readme @@ -0,0 +1,554 @@ +!=========================================================================== +! LIMITS NAMELIST +! +! CONTENTS: +! +! NDAY1 : First day of integration (i) +! NDAY2 : Last day of integration (i) +! IDATE : Model date in YYYYMMDD (i) +! IDATE0 : Initial experiment date in YYYYMMDD (i) +! RUNID : Experiment name (a) +! EXPCNF : Experiment configuration (a) +! RUNTYP : CESM run type (a) +! GRFILE : Name of file containing grid specification (a) +! ICFILE : Name of file containing initial conditions, that is either +! a valid restart file or 'inicon.nc' if climatological based +! initial conditions are desired (a) +! PREF : Reference pressure for potential density (g/cm/s2) (f) +! BACLIN : Baroclinic time step (sec) (f) +! BATROP : Barotropic time step (sec) (f) +! MDV2HI : Laplacian diffusion velocity for momentum dissipation (cm/s) (f) +! MDV2LO : Laplacian diffusion velocity for momentum dissipation (cm/s) (f) +! MDV4HI : Biharmonic diffusion velocity for momentum dissipation (cm/s) (f) +! MDV4LO : Biharmonic diffusion velocity for momentum dissipation (cm/s) (f) +! MDC2HI : Laplacian diffusivity for momentum dissipation (cm**2/s) (f) +! MDC2LO : Laplacian diffusivity for momentum dissipation (cm**2/s) (f) +! VSC2HI : Parameter in deformation-dependent Laplacian viscosity (f) +! VSC2LO : Parameter in deformation-dependent Laplacian viscosity (f) +! VSC4HI : Parameter in deformation-dependent Biharmonic viscosity (f) +! VSC4LO : Parameter in deformation-dependent Biharmonic viscosity (f) +! CBAR : rms flow speed for linear bottom friction law (cm/s) (f) +! CB : Nondiemnsional coefficient of quadratic bottom friction (f) +! CWBDTS : Coastal wave breaking damping resiprocal time scale (1/s) (f) +! CWBDLS : Coastal wave breaking damping length scale (m) (f) +! MOMMTH : Momentum equation discretization method. Valid methods: +! 'enscon' (Sadourny (1975) enstrophy conserving), 'enecon' +! (Sadourny (1975) energy conserving), 'enedis' (Sadourny +! (1975) energy conserving with some dissipation) (a) +! BMCMTH : Baroclinic mass flux correction method. Valid methods: +! 'uc' (upstream column), 'dluc' (depth limited upstream +! column) (a) +! RMPMTH : Method of applying eddy-induced transport in the remap +! transport algorithm. Valid methods: 'eitvel', 'eitflx' (a) +! MLRTTP : Type of mixed layer restratification time scale. Valid +! types: 'variable', 'constant', 'limited' (a) +! RM0 : Efficiency factor of wind TKE generation in the Oberhuber +! (1993) TKE closure () (f) +! RM5 : Efficiency factor of TKE generation by momentum +! entrainment in the Oberhuber (1993) TKE closure () (f) +! CE : Efficiency factor for the restratification by mixed layer +! eddies (Fox-Kemper et al., 2008) () (f) +! TDFILE : Name of file containing tidal wave energy dissipation +! divided by by bottom buoyancy frequency (a) +! NIWGF : Global factor applied to the energy input by near-intertial +! motions () (f) +! NIWBF : Fraction of near-inertial energy dissipated in the boundary +! layer () (f) +! NIWLF : Fraction of near-inertial energy dissipated locally beneath +! the boundary layer () (f) +! SWAMTH : Shortwave radiation absorption method. Valid methods: +! 'top-layer', 'jerlov', 'chlorophyll' (a) +! JWTYPE : Number indicating the Jerlov (1968) water type (i) +! CHLOPT : Chlorophyll concentration option. Valid options: +! 'climatology' (a) +! CCFILE : Name of file containing chlorophyll concentration climatology (a) +! TRXDAY : e-folding time scale (days) for SST relax., if 0 no relax. (f) +! SRXDAY : e-folding time scale (days) for SSS relax., if 0 no relax. (f) +! TRXDPT : Maximum mixed layer depth for e-folding SST relaxation (m) (f) +! SRXDPT : Maximum mixed layer depth for e-folding SSS relaxation (m) (f) +! TRXLIM : Max. absolute value of SST difference in relaxation (degC) (f) +! SRXLIM : Max. absolute value of SSS difference in relaxation (psu) (f) +! APTFLX : Apply diagnosed heat flux flag (l) +! APSFLX : Apply diagnosed freshwater flux flag (l) +! DITFLX : Diagnose heat flux flag (l) +! DISFLX : Diagnose freshwater flux flag (l) +! SRXBAL : Balance the SSS relaxation (l) +! SCFILE : Name of file containing SSS climatology used for relaxation (a) +! WAVSRC : Source of wave fields. Valid source: 'none', 'param', 'extern' (a) +! SMTFRC : Smooth CESM forcing (l) +! SPRFAC : Send precipitation/runoff factor to CESM coupler (l) +! ATM_PATH : Path to forcing fields in case of EXPCNF 'ben02clim' or +! 'ben02syn' (a) +! ITEST : Global i-index of point diagnostics (i) +! JTEST : Global j-index of point diagnostics (i) +! CNSVDI : Conservation diagnostics flag (l) +! CSDIAG : Checksum diagnostics flag (l) +! RSTFRQ : Restart frequency in days (30=1month,365=1year) (i) +! RSTFMT : Format of restart file (valid arguments are 0 for classic, +! 1 for 64-bit offset and 2 for netcdf4/hdf5 format) (i) +! RSTCMP : Compression flag for restart file (i) +! IOTYPE : 0 = netcdf, 1 = pnetcdf + +!=========================================================================== +! NAMELIST FOR DIFFUSION PARAMETERS +! +! CONTENTS: +! +! EITMTH : Eddy-induced transport parameterization method. Valid +! methods: 'intdif', 'gm' (a) +! EDRITP : Type of Richardson number used in eddy diffusivity +! computation. Valid types: 'shear', 'large scale' (a) +! EDWMTH : Method to estimate eddy diffusivity weight as a function of +! the ration of Rossby radius of deformation to the +! horizontal grid spacing. Valid methods: 'smooth', 'step' (a) +! MLRTTP : Type of mixed layer restratification time scale. Valid +! types: 'variable', 'constant', 'limited' (a) +! EDDF2D : If true, eddy diffusivity has a 2d structure (l) +! EDSPRS : Apply eddy mixing suppression away from steering level (l) +! EGC : Parameter c in Eden and Greatbatch (2008) parameterization (f) +! EGGAM : Parameter gamma in E. & G. (2008) param. (f) +! EGLSMN : Minimum eddy length scale in E. & G. (2008) param. (cm) (f) +! EGMNDF : Minimum diffusivity in E. & G. (2008) param. (cm**2/s) (f) +! EGMXDF : Maximum diffusivity in E. & G. (2008) param. (cm**2/s) (f) +! EGIDFQ : Factor relating the isopycnal diffusivity to the layer +! interface diffusivity in the Eden and Greatbatch (2008) +! parameterization. egidfq=difint/difiso () (f) +! TBFILE : Name of file containing topographic beta parameter (a) +! RHISCF : Linear scaling parameter for topographic rhines scale () (f) +! EDANIS : If true, apply anisotropy correction to eddy diffusivity (l) +! REDI3D : If true, then isopycnal/neutral diffusion will have 3D +! structure based in the 3D structure of anisotropy (l) +! RHSCTP : If true, use the minimum of planetary and topographic beta +! to define the Rhines scale (l) +! RI0 : Critical gradient richardson number for shear driven +! vertical mixing () (f) +! BDMTYP : Type of background diapycnal mixing. If bdmtyp=1 the +! background diffusivity is a constant divided by the +! Brunt-Vaisala frequency, if bdmtyp=2 the background +! diffusivity is constant () (i) +! BDMC1 : Background diapycnal diffusivity times buoyancy frequency +! frequency (cm**2/s**2) (f) +! BDMC2 : Background diapycnal diffusivity (cm**2/s) (f) +! BDMLDP : Make the background mixing latitude dependent according to +! Gregg et al. (2003) (l) +! TKEPF : Fraction of surface TKE that penetrates beneath mixed layer +! () (f) +! SMOBLD : If true, apply lateral smoothing of CVMix estimated +! boundary layer depth (l) +! LNGMTP : Type of CVMix Langmuir turbulence parameterization. Valid +! types: 'none', 'vr12-ma', 'lf17' +! LTEDTP : Type of lateral tracer eddy diffusion: Valid methods: +! 'layer', 'neutral'. + +!=========================================================================== +! NAMELIST FOR CHANNEL WIDTH MODIFICATIONS +! +! CONTENTS: +! +! CWMTAG : Array of geographical names of channels to be modified (a) +! CWMEDG : Array of C grid cell edges to be modified. Valid options: +! 'u' or 'v' (a) +! CWMI : Array of grid cell i-indices (i) +! CWMJ : Array of grid cell j-indices (i) +! CWMWTH : Array of modified grid cell widths (m) (f) +! +!=========================================================================== +! NAMELIST FOR MERIDIONAL OVERTURNING AND FLUX DIAGNOSTICS +! +! CONTENTS: +! +! MER_ORFILE : Name of file containing ocean region specification (a) +! MER_MIFILE : Name of file containing zonal section specification for +! meridional transport computation (a) +! MER_REGNAM : Array of region names for meridional overturning and flux +! diagnostics (a) +! MER_REGFLG : Array of mask flags in ocean regions file to be included +! for each region (i) +! MER_MINLAT : Minimum latitude to be considered for each region (f) +! MER_MAXLAT : Maximum latitude to be considered for each region (f) +! +!=========================================================================== +! NAMELIST FOR SECTION TRANSPORT DIAGNOSTICS +! +! CONTENTS: +! +! SEC_SIFILE : Name of file containing section specification for section +! transport computation (a) +! +!=========================================================================== +! IO-NAMELIST FOR DIAGNOSTIC OUTPUT +! +! Description: +! BLOM supports multiple output groups for its diagnostic output. +! Each output group is represented by one column in the namlist and may +! have its own output format, averaging period, and file frequency. +! The maximum number of output groups is currently limited to 10 but +! can be changed easily in mod_dia.F. +! +! The output precision can be choosen on a per-variable basis. +! +! Multiple time-slices can be written to the same output file +! provided that no variable is written in packed data format +! (i.e. as int2 with scale factor and offset). +! +! Compression of the output (i.e. storage of only wet points) +! and the file format can be choosen on a per-file basis. +! +! All time periods are specified in number of days for positive +! integer values and fraction of day for negative integer values. +! The length of the actual calendar month is used if 30 is written. +! The length of the actual calendar year is used if 365 is written. +! A variable is not written when 0 is specified. +! +! Namelist acronyms: +! GLB_ - global parameters i.e. valid for entire output group +! H2D_ - 2d fields with the horizontal dimensions +! LYR_ - 3d fields with sigma layers as vertical coordinate +! LVL_ - 3d fields with levitus leves as vertical coordinate +! MSC_ - miscellanous, non-gridded fields +! +! Global parameters: +! FNAMETAG - tag used in file name (c10) +! AVEPERIO - average period in days (i) +! FILEFREQ - how often to start a new file in days (i) +! COMPFLAG - switch for compressed/uncompressed output (i) +! NCFORMAT - netcdf format (valid arguments are 0 for classic, +! 1 for 64-bit offset and 2 for netcdf4/hdf5 format) +! +! Arguments for diagnostic variables: +! 0 - variable is not written +! 2 - variable is written as int2 with scale factor and offset +! 4 - variable is written as real4 +! 8 - variable is written as real8 +! +! Output variables: +! ABSWND - absolute wind speed [m s-1] +! ALB - surface albedo [] +! BTMSTR - Barotropic mass streamfunction [kg s-1] +! BRNFLX - brine flux [kg m-2 s-1] +! BRNPD - brine plume depth [m] +! DFL - non-solar heat flux derivative [W m-2 K-1] +! EVA - evaporation [kg m-2 s-1] +! FICE - ice concentration [%] +! FMLTFZ - fresh water flux due to melting/freezing [kg m-2 s-1] +! HICE - ice thickness [m] +! HMLTFZ - heat flux due to melting/freezing [W m-2] +! HSNW - snow depth [m] +! IAGE - ice age [d] +! IDKEDT - mixed layer inertial kinetic energy tendency [kg s-3] +! LAMULT - Langmuir enhancement factor [] +! LASL - Surface layer averaged Langmuir number [] +! LIP - liquid precipitation [kg m-2 s-1] +! MAXMLD - maximum mixed layer depth [m] +! MLD - mixed layer depth [m] +! MLTS - mixed layer thickness using "sigma-t" criterion [m] +! MLTSMN - minimum mixed layer thickness using "sigma-t" criterion [m] +! MLTSMX - maximum mixed layer thickness using "sigma-t" criterion [m] +! MLTSSQ - mixed layer thickness squared using "sigma-t" criterion [m2] +! MTKEUS - mixed layer TKE tendency related to friction velocity [kg s-3] +! MTKENI - mixed layer TKE tendency related to near inertial mot. [kg s-3] +! MTKEBF - mixed layer TKE tendency related to buoyancy forcing [kg s-3] +! MTKERS - mixed layer TKE tendency related to eddy restrat. [kg s-3] +! MTKEPE - mixed layer TKE tendency related to pot. energy change [kg s-3] +! MTKEKE - mixed layer TKE tendency related to kin. energy change [kg s-3] +! MTY - wind stress y-component [N m-2] +! NSF - non-solar heat flux [W m-2] +! PBOT - bottom pressure [Pa] +! PSRF - surface pressure [Pa] +! RFIFLX - frozen runoff [kg m-2 s-1] +! RNFFLX - liquid runoff [kg m-2 s-1] +! SALFLX - salt flux received by ocean [kg m-2 s-1] +! SALRLX - restoring salt flux received by ocean [kg m-2 s-1] +! SBOT - bottom salinity [g kg-1] +! SEALV - sea level [m] +! SLVSQ - sea level squared [m2] +! SFL - salt flux [kg m-2 s-1] +! SOP - solid precipitation [kg m-2 s-1] +! SIGMX - mixed layer density [kg m-3] +! SSS - ocean surface salinity [g kg-1] +! SSSSQ - ocean surface salinity squared [g2 kg-2] +! SST - ocean surface temperature [degC] +! SSTSQ - ocean surface temperature squared [degC2] +! SURFLX - heat flux received by ocean [W m-2] +! SURRLX - restoring heat flux received by ocean [W m-2] +! SWA - short-wave heat flux [W m-2] +! T20D - 20C isoterm depth [m] +! TAUX - momentum flux received by ocean x-component [N m-2] +! TAUY - momentum flux received by ocean y-component [N m-2] +! TBOT - bottom temperature [degC] +! TICE - ice temperature [degC] +! TSRF - surface temperature [degC] +! UB - barotropic velocity x-component [m s-1] +! UICE - ice velocity x-component [m s-1] +! USTAR - friction velocity [m s-1] +! USTAR3 - friction velocity cubed [m3 s-3] +! USTOKES - surface Stokes drift x-componen [m s-1] +! VB - barotropic velocity y-component [m s-1] +! VICE - ice velocity y-component [m s-1] +! VSTOKES - surface Stokes drift y-componen [m s-1] +! ZTX - wind stress x-component [N m-2] +! BFSQ - buoyancy frequency squared [s-1] +! DIFDIA - vertical diffusivity [log10(m2 s-1)|m2 s-1] +! DIFVMO - vertical momentum diffusivity [log10(m2 s-1)|m2 s-1] +! DIFVHO - vertical heat diffusivity [log10(m2 s-1)|m2 s-1] +! DIFVSO - vertical salt diffusivity [log10(m2 s-1)|m2 s-1] +! DIFINT - layer interface diffusivity [log10(m2 s-1)] +! DIFISO - isopycnal diffusivity [log10(m2 s-1)] +! DP - layer pressure thickness [Pa] +! DZ - layer thickness [m] +! SALN - salinity [g kg-1] +! TEMP - temperature [degC] +! TRC - tracer [] +! UFLX - mass flux in x-direction [kg s-1] +! UTFLX - heat flux in x-direction [W] +! USFLX - salt flux in x-direction [kg s-1] +! UMFLTD - mass flux due to thickness diffusion in x-direction [kg s-1] +! UMFLSM - mass flux due to submesoscale transport in x-direction [kg s-1] +! UTFLTD - heat flux due to thickness diffusion in x-direction [W] +! UTFLSM - heat flux due to submesoscale transport in x-direction [W] +! UTFLLD - heat flux due to lateral diffusion in x-direction [W] +! USFLTD - salt flux due to thickness diffusion in x-direction [kg s-1] +! USFLSM - salt flux due to submesoscale transport in x-direction [kg s-1] +! USFLLD - salt flux due to lateral diffusion in x-direction [kg s-1] +! UVEL - velocity x-component [m s-1] +! VFLX - mass flux in y-direction [kg s-1] +! VTFLX - heat flux in y-direction [W] +! VSFLX - salt flux in y-direction [kg s-1] +! VMFLTD - mass flux due to thickness diffusion in y-direction [kg s-1] +! VMFLSM - mass flux due to submesoscale transport in y-direction [kg s-1] +! VTFLTD - heat flux due to thickness diffusion in y-direction [W] +! VTFLSM - heat flux due to submesoscale transport in y-direction [W] +! VTFLLD - heat flux due to lateral diffusion in y-direction [W] +! VSFLTD - salt flux due to thickness diffusion in y-direction [kg s-1] +! VSFLSM - salt flux due to submesoscale transport in y-direction [kg s-1] +! VSFLLD - salt flux due to lateral diffusion in y-direction [kg s-1] +! VVEL - velocity x-component [m s-1] +! WFLX - vertical mass flux [kg s-1] +! WFLX2 - vertical mass flux squared [kg2 s-2] +! PV - potential vorticity [m-1 s-1] +! TKE - turbulent kinetic energy [m2 s-2] +! GLS_PSI - generic length scale [m2 s-3] +! IDLAGE - ideal age [year] +! MMFLXL - meridional overturning circ. (MOC) on isopycnic layers [kg s-1] +! MMFLXD - MOC on z-levels [kg s-1] +! MMFTDL - MOC due to thickness diffusion on isopycnic layers [kg s-1] +! MMFSML - MOC due to submesoscale transport on isopycnic layers [kg s-1] +! MMFTDD - MOC due to thickness diffusion on z-levels [kg s-1] +! MMFSMD - MOC due to submesoscale transport on z-levels [kg s-1] +! MHFLX - meridional heat flux [W] +! MHFTD - meridional heat flux due to thickness diffusion [W] +! MHFSM - meridional heat flux due to submesoscale transport [W] +! MHFLD - meridional heat flux due to lateral diffusion [W] +! MSFLX - meridional salt flux [kg s-1] +! MSFTD - meridional salt flux due to thickness diffusion [kg s-1] +! MSFSM - meridional salt flux due to submesoscale transport [kg s-1] +! MSFLD - meridional salt flux due to lateral diffusion [kg s-1] +! VOLTR - section transports [kg s-1] +! MASSGS - global sum of mass [kg] +! VOLGS - global sum of volume [m3] +! SALNGA - global average temperature [degC] +! TEMPGA - global average temperature [degC] +! SSSGA - global average sea surface salinity [g kg-1] +! SSTGA - global average sea surface temperature [degC] +! +!=========================================================================== +! NAMELIST FOR iHAMOCC OPTIONS +! +! CONTENTS: +! +! ATM_CO2 : Atmospheric CO2 concentration [ppmv] +! FEDEPFILE : File name (incl. full path) for iron (dust) deposition data +! SWACLIMFILE : File name (incl. full path) for swa climatology field (needed +! if bromoform scheme is activated) +! DO_RIVINPT : Logical switch to activate riverine input +! RIVINFILE : File name (incl. full path) for riverine input data +! DO_NDEP : Logical switch to activate N-deposition +! NDEPFILE : File name (incl. full path) for atmopheric N-deposition data +! DO_SEDSPINUP: Logical switch to activate sediment spin-up +! SEDSPIN_YR_S: Start year for sediment spinup +! SEDSPIN_YR_E: End year for sediment spinup +! SEDSPIN_NCYC: Number of subcyles per time-step for sediment spinup +! INIXXX : Initial condition file for iHAMOCC, where XXX=DIC, ALK, PO4, +! OXY, NO3, SIL, D13C, and D14C +! WITH_DMSPH : Logical switch to activate DMS calculation as function of pH +! PI_PH_FILE : File name (incl. full path) for surface PI pH input data. +! L_3DVARSEDPOR : Logical switch to enable lon-lat-depth variable sediment porosity (as opposed to default: only depth) +! SEDPORFILE : File name (incl. full path) for sediment porosity +! +!=========================================================================== +! NAMELIST FOR ALKALINIZATION SCENARIO +! +! CONTENTS: +! +! OALKSCEN : Name of alkalinization scenario ('const', 'ramp', or 'file') +! OALKFILE : Full path of the input file for the alkalinization scenario 'file' +! ADDALK : Pmol alkalinity/yr added in 'const' or 'ramp' scenarios +! CDRMIP_LATMAX : Max latitude where alkalinity is added in 'const' or 'ramp' scenarios +! CDRMIP_LATMIN : Min latitude where alkalinity is added in 'const' or 'ramp' scenarios +! RAMP_START : Start year for ramp up in 'ramp' scenario +! RAMP_END : End year for ramp up in 'ramp' scenario +! +!=========================================================================== +! IO-NAMELIST FOR DIAGNOSTIC iHAMOCC OUTPUT +! +! Namelist acronyms: +! GLB_ - global parameters i.e. valid for entire output group +! SRF_ - surface variables (includes some non-surface 2d fields) +! FLX_ - interior ocean particle fuxes at different depth (2d) +! INT_ - vertically integrated fields (2d) +! LYR_ - 3d fields with sigma layers as vertical coordinate +! LVL_ - 3d fields with levitus levels as vertical coordinate +! SDM_ - 3d sediment fields +! BUR_ - 2d fields of sediment burial +! +! Global parameters: +! FNAMETAG - tag used in file name (c10) +! AVEPERIO - average period in days (i) +! FILEFREQ - how often to start a new file in days (i) +! COMPFLAG - switch for compressed/uncompressed output (i) +! NCFORMAT - netcdf format (valid arguments are 0 for classic, +! 1 for 64-bit offset and 2 for netcdf4/hdf5 format) +! INVENTORY- how often to write an inventory of tracers to ocean +! output file: +! 0 : no output +! 1 : write inventory to standard output (log file) +! 2 : write output to inventory netCDF file +! +! Arguments for diagnostic variables: +! 0 - variable is not written +! 2 - variable is written as int2 with scale factor and offset +! 4 - variable is written as real4 +! 8 - variable is written as real8 +! +! Output variables: +! +! Main BGC tracer fields (SFR, LYR or LVL) +! DIC - Dissolved carbon (dissic) [mol C m-3] +! ALKALI - Alkalinity (talk) [eq m-3] +! OXYGEN - Oxygen (o2) [mol O2 m-3] +! ANO3 - Nitrate (no3) [mol N m-3] +! PHOSPH - Phosphorus (po4) [mol P m-3] +! IRON - Dissolved iron (dfe) [mol Fe m-3] +! SILICA - Silicate (si) [mol Si m-3] +! PHYTO - Phytoplankton (phyc) [mol C m-3] +! PH - pH (ph) [-log10([h+])] +! NATDIC - Natural dissolved carbon (natdissic) [mol C m-3] +! NATALKALI - Natural alkalinity (nattalk) [eq m-3] +! NATPH - Natural pH (natph) [-log10([h+])] +! +! Other 3d tracer or diagnostic variables (LYR or LVL) +! DP - Layer thickness (pddpo) [m] +! PREFO2 - preformed oxygen (p_o2) [mol O2 m-3] +! O2SAT - Saturated oxygen (satoxy) [mol O2 m-3] +! PREFPO4 - preformed phosphate (p_po4) [mol PO4 m-3] +! PREFALK - preformed alkalinity (p_talk) [eq m-3] +! PREFDIC - preformed DIC (p_dic) [mol C m-3] +! DICSAT - saturated DIC (dic_sat) [mol C m-3] +! POC - Detrius (detoc) [mol C m-3] +! CALC - CaCO3 shells (calc) [mol C m-3] +! OPAL - Opal shells (opal) [mol Si m-3] +! DOC - Dissolved organic carbon (dissoc) [mol C m-3] +! GRAZER - Zooplankton (zooc) [mol C m-3] +! PHOSY - Primary production (pp) [mol C m-3 s-1] +! CO3 - Carbonate ions (co3) [mol C m-3] +! N2O - Nitrous oxide concentration [mol N2O m-3] +! OMEGAA - Aragonite saturation state (omegaa) [1] +! OMEGAC - Calcite saturation state (omegac) [1] +! NATDIC - Natural dissolved carbon (natdissic) [mol C m-3] +! NATALKALI - Natural alkalinity (nattalk) [eq m-3] +! NATCO3 - Natural carbonate ion concentration (natco3) [mol C m-3] +! NATCALC - Natural CaCO3 shells (natcalc) [mol C m-3] +! NATOMEGAA - Natural aragonite saturation state (natomegaa) [1] +! NATOMEGAC - Natural calcite saturation state (natomegac) [1] +! DIC13 - Dissolved C13 (dissic13) [mol C m-3] +! DIC14 - Dissolved C14 (dissic14) [mol C m-3] +! D13C - delta 13C of DIC [1] +! D14C - delta 14C of DIC [1] +! BIGD14C - Delta 14C of DIC [1] +! POC13 - Particulate organic carbon 13 (detoc13) [mol C m-3] +! DOC13 - Dissolved organic carbon 13 (dissoc13) [mol C m-3] +! CALC13 - Particulate inorganic carbon 13 (calc13) [mol C m-3] +! PHYTO13 - 13C of phytoplankton biomass (phyc13) [mol C m-3] +! GRAZER13 - 13C of zootoplankton biomass (zooc13) [mol C m-3] +! CFC11 - CFC11 concentration [mol CFC11 m-3] +! CFC12 - CFC12 concentration [mol CFC12 m-3] +! SF6 - SF6 concentration [mol SF6 m-3] +! NOS - Number of sinking particles (aggregate scheme, nos) [cm-3] +! WPHY - Mass sinking velocity (aggregate scheme) [m d-1] +! WNOS - Number sinking velocity (aggregate scheme) [m d-1] +! EPS - Epsilon exponent (aggregate scheme) [1] +! ASIZE - Average particle size (aggregate scheme) +! +! 2d-fields (SFR) +! EXPORT - Export production (epc100) [mol C m-2 s-1] +! EXPOCA - Ca export production (epcalc100) [mol Ca m-2 s-1] +! EXPOSI - Si export production (epsi100) [mol Si m-2 s-1] +! PCO2 - Surface PCO2 (spco2) [uatm] +! PCO2M - Surface PCO2 under moist air assumption [uatm] +! KWCO2 - Piston velocity (kwco2) [m s-1] +! KWCO2KHM - Piston velocity times solubility (kwco2*kh; moist air) [m s-1 mol kg-1 uatm-1] +! CO2KH - CO2 solubility under dry air assumption (khd) [mol kg-1 atm-1] +! CO2KHM - CO2 solubility under moist air assumption (kh) [mol kg-1 atm-1] +! CO2FXD - Downward CO2 flux (co2fxd) [kg C m-2 s-1] +! CO2FXU - Upward CO2 flux (co2fxu) [kg C m-2 s-1] +! NIFLUX - Nitrogen flux (fgn2) [mol N2 m-2 s-1] +! OXFLUX - Oxygen flux (fgo2) [mol O2 m-2 s-1] +! N2OFX - Nitrous oxide flux [mol N2O m-2 s-1] +! DMSFLUX - DMS flux (dmsflux) [mol DMS m-2 s-1] +! DMS - surface DMS concentration (dms) [mol DMS m-3] +! DMSPROD - DMS production (dmsprod) [mol DMS m-2 s-1] +! DMS_BAC - DMS bacterial consuption (dms_bac) [mol DMS m-2 s-1] +! DMS_UV - DMS decomposition by UV (dms_uv) [mol DMS m-2 s-1] +! ATMCO2 - Atmospheric CO2 (atmco2) [ppm] +! ATMO2 - Atmospheric O2 (atmo2) [ppm] +! ATMN2 - Atmospheric N2 (atmn2) [ppm] +! NATPCO2 - Natural surface PCO2 (spco2) [uatm] +! NATCO2FX - Natural net CO2 flux (natco2fx) [kg C m-2 s-1] +! CO213FXD - Downward 13CO2 flux (co213fxd) [kg C m-2 s-1] +! CO213FXU - Upward 13CO2 flux (co213fxu) [kg C m-2 s-1] +! CO214FXD - Downward 14CO2 flux (co214fxd) [kg C m-2 s-1] +! CO214FXU - Upward 14CO2 flux (co214fxu) [kg C m-2 s-1] +! CFC11 - CFC11 flux [mol CFC11 m-2 s-1] +! CFC12 - CFC12 flux [mol CFC12 m-2 s-1] +! SF6 - SF6 flux [mol SF6 m-2 s-1] +! +! Vertically integrated fields (INT) +! PHOSY - Vertically integrated primary production [mol C m-3 s-1] +! NFIX - Vertically integrated nitrogen fixation +! DNIT - Vertically integrated denitrification +! +! Particle fluxes (FLX, e.g CARFLX****, where ****=0100,0500,1000,2000,4000, or _BOT), +! diffusive fluxes at the sediment - water-column interface (SEDIFF*), and other fluxes +! NDEP - Nitrogen deposition flux [mol N m-2 s-1] +! OALK - Flux of alkalinity due to ocean alkalinization [mol N m-2 s-1] +! CARFLX**** - POC flux at **** metres depth [mol C m-2 s-1] +! BSIFLX**** - Biogenic silica flux at **** metres depth [mol Si m-2 s-1] +! CALFLX**** - Calcium carbonate flux at **** metres depth [mol C m-2 s-1] +! SEDIFFIC - sediment - water-column diffusive flux of DIC [mol C m-2 s-1] +! SEDIFFAL - sediment - water-column diffusive flux of alkalinity [mol m-2 s-1] +! SEDIFFPH - sediment - water-column diffusive flux of phosphate [mol PO3 m-2 s-1] +! SEDIFFOX - sediment - water-column diffusive flux of oxygen [mol O2 m-2 s-1] +! SEDIFFN2 - sediment - water-column diffusive flux of N2 [mol N2 m-2 s-1] +! SEDIFFNO3 - sediment - water-column diffusive flux of nitrate [mol NO3 m-2 s-1] +! SEDIFFSI - sediment - water-column diffusive flux of silica [mol Si m-2 s-1] +! +! Sediment fields (SDM) +! POWAIC - (powdic) [mol C m-3] +! POWAAL - (powalk) [eq m-3] +! POWAPH - (powpho) [eq m-3] +! POWAOX - (powox) [mol O2 m-3] +! POWN2 - (pown2) [mol N2 m-3] +! POWNO3 - (powno3)[mol N m-3] +! POWASI - (powsi) [mol Si m-3] +! SSSO12 - (ssso12) [mol m-3] +! SSSSIL - (ssssil) [mol Si m-3] +! SSSC12 - (sssc12) [mol C m-3] +! SSSTER - (ssster) [mol m-3] +! +! Burial fields (BUR) +! SSSO12 - Solid sediment organic carbon [mol P m-2] +! SSSSIL - Solid sediment silica [mol Si m-2] +! SSSC12 - Solid sediment inorganic carbon [mol C m-2] +! SSSTER - +! +!=========================================================================== From e8205fbd13bf899e0625556dcb8bacb3b57de2c3 Mon Sep 17 00:00:00 2001 From: Mariana Vertenstein Date: Wed, 26 Jul 2023 11:33:02 +0200 Subject: [PATCH 4/6] rename of aux tests --- cime_config/testdefs/testlist_blom.xml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/cime_config/testdefs/testlist_blom.xml b/cime_config/testdefs/testlist_blom.xml index 5704bcc4..5799fbb6 100644 --- a/cime_config/testdefs/testlist_blom.xml +++ b/cime_config/testdefs/testlist_blom.xml @@ -2,22 +2,22 @@ - + - + - + - + From de96479e2bfe66b2a3100e30107fb1da05b06463 Mon Sep 17 00:00:00 2001 From: Mariana Vertenstein Date: Wed, 26 Jul 2023 15:23:50 +0200 Subject: [PATCH 5/6] update to PE layout to resolve issue #258 --- cime_config/config_pes.xml | 38 +++++++++++++------------- cime_config/testdefs/testlist_blom.xml | 7 ++++- 2 files changed, 25 insertions(+), 20 deletions(-) diff --git a/cime_config/config_pes.xml b/cime_config/config_pes.xml index d561156d..a7f93d71 100644 --- a/cime_config/config_pes.xml +++ b/cime_config/config_pes.xml @@ -118,14 +118,14 @@ none - 1 - 1 - 96 + 128 + 128 + 128 354 - 126 - 1 - 1 - 1 + 128 + 128 + 128 + 128 1 @@ -138,11 +138,11 @@ 1 - 96 - 97 - 98 + 0 + 0 + 0 0 - 126 + 128 0 0 0 @@ -155,14 +155,14 @@ none - 192 - 192 - 192 + 128 + 128 + 128 354 - 192 - 1 - 1 - 1 + 128 + 128 + 128 + 128 1 @@ -179,7 +179,7 @@ 0 0 0 - 192 + 128 0 0 0 diff --git a/cime_config/testdefs/testlist_blom.xml b/cime_config/testdefs/testlist_blom.xml index 5799fbb6..f54c99eb 100644 --- a/cime_config/testdefs/testlist_blom.xml +++ b/cime_config/testdefs/testlist_blom.xml @@ -1,6 +1,11 @@ - + + + + + + From 537fb0139f8a8d0cc8765588f933ef1b6eaaf9e0 Mon Sep 17 00:00:00 2001 From: Mariana Vertenstein Date: Fri, 28 Jul 2023 10:40:10 +0200 Subject: [PATCH 6/6] fixed history file name when daily output is needed for cesm testing --- cime_config/config_component.xml | 2 +- phy/mod_dia.F | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/cime_config/config_component.xml b/cime_config/config_component.xml index 8ed52757..a38225a8 100644 --- a/cime_config/config_component.xml +++ b/cime_config/config_component.xml @@ -211,7 +211,7 @@ TRUE,FALSE FALSE - TRUE + TRUE build_component_blom env_build.xml diff --git a/phy/mod_dia.F b/phy/mod_dia.F index f06e4f03..6e63f492 100644 --- a/phy/mod_dia.F +++ b/phy/mod_dia.F @@ -369,7 +369,7 @@ subroutine diafnm(ctag,diagfq,diagmon,diagann,fname) . date_tmp%year,sep2,date_tmp%month,'.nc' else write(fname,'(4a,i4.4,a,i2.2,a,i2.2,a)') - . trim(runid),sep1,trim(ctag),sep1, + . trim(prefix),sep1,trim(ctag),sep1, . date_tmp%year,sep2,date_tmp%month,sep2,date_tmp%day,'.nc' endif else @@ -386,7 +386,7 @@ subroutine diafnm(ctag,diagfq,diagmon,diagann,fname) endif ns=86400*(mod(nstep-1,nstep_in_day)+1)/nstep_in_day write(fname,'(4a,i4.4,a,i2.2,a,i2.2,a,i5.5,a)') - . trim(runid),sep1,trim(ctag),sep1, + . trim(prefix),sep1,trim(ctag),sep1, . date_tmp%year,sep2,date_tmp%month,sep2,date_tmp%day,sep2,ns, . '.nc' endif