Merge pull request NOAA-EMC#20 from jkhender/feature/chem

additional changes to run in realtime

.gitignore

@@ -1,15 +1,175 @@
 # Ignore all compiled files
+__pycache__
 *.pyc
 *.o
 *.mod
 
 # Ignore exec folder
 exec/
 
-# Ignore sorc folders from externals
-sorc/logs/
-sorc/fv3gfs.fd/
-sorc/gsi.fd/
-sorc/ufs_utils.fd/
-sorc/gfs_wafs.fd/
-sorc/verif-global.fd/
+# Ignore fix directory symlinks
+fix/0readme
+fix/fix_*
+fix/gdas/
+fix/wafs
+
+# Ignore sorc and logs folders from externals
+sorc/*log
+sorc/logs
+sorc/fv3gfs.fd
+sorc/fv3gfs_ccpp_chem.fd
+sorc/gfs_post.fd
+sorc/gsi.fd
+sorc/ufs_utils.fd
+sorc/gfs_wafs.fd
+sorc/verif-global.fd
+sorc/prepchem_NC.fd
+
+# Ignore sorc symlinks
+sorc/calc_analysis.fd
+sorc/calc_increment_ens.fd
+sorc/calc_increment_ens_ncio.fd
+sorc/chgres_cube.fd
+sorc/emcsfc_ice_blend.fd
+sorc/emcsfc_snow2mdl.fd
+sorc/filter_topo.fd
+sorc/fregrid.fd
+sorc/gdas2gldas.fd
+sorc/getsfcensmeanp.fd
+sorc/getsigensmeanp_smooth.fd
+sorc/getsigensstatp.fd
+sorc/gfs_ncep_post.fd
+sorc/gldas.fd
+sorc/gldas2gdas.fd
+sorc/gldas_forcing.fd
+sorc/gldas_model.fd
+sorc/gldas_post.fd
+sorc/gldas_rst.fd
+sorc/global_chgres.fd
+sorc/global_cycle.fd
+sorc/global_enkf.fd
+sorc/global_gsi.fd
+sorc/interp_inc.fd
+sorc/make_hgrid.fd
+sorc/make_solo_mosaic.fd
+sorc/mkgfsnemsioctl.fd
+sorc/nemsio_chgdate.fd
+sorc/nemsio_get.fd
+sorc/nemsio_read.fd
+sorc/nst_tf_chg.fd
+sorc/orog.fd
+sorc/oznmon_horiz.fd
+sorc/oznmon_time.fd
+sorc/radmon_angle.fd
+sorc/radmon_bcoef.fd
+sorc/radmon_bcor.fd
+sorc/radmon_time.fd
+sorc/recentersigp.fd
+sorc/shave.fd
+sorc/wafs_awc_wafavn.fd
+sorc/wafs_blending.fd
+sorc/wafs_cnvgrib2.fd
+sorc/wafs_gcip.fd
+sorc/wafs_makewafs.fd
+sorc/wafs_setmissing.fd
+
+# Ignore parm file symlinks
+parm/config/config.base
+parm/gldas
+parm/mon
+parm/post
+parm/wafs
+
+# Ignore scripts from externals
+jobs/JGDAS_ENKF_CHGRES
+jobs/JGDAS_ENKF_FCST
+jobs/JGDAS_ENKF_POST
+jobs/JGDAS_ENKF_RECENTER
+jobs/JGDAS_ENKF_SURFACE
+jobs/JGDAS_GLDAS
+jobs/JGDAS_VERFOZN
+jobs/JGDAS_VERFRAD
+jobs/JGDAS_VMINMON
+jobs/JGFS_VMINMON
+jobs/JGFS_WAFS
+jobs/JGFS_WAFS_BLENDING
+jobs/JGFS_WAFS_GCIP
+jobs/JGFS_WAFS_GRIB2
+jobs/JGLOBAL_ANALCALC
+jobs/JGLOBAL_ANALDIAG
+jobs/JGLOBAL_ANALYSIS
+jobs/JGLOBAL_ENKF_ANALDIAG
+jobs/JGLOBAL_ENKF_INNOVATE_OBS
+jobs/JGLOBAL_ENKF_SELECT_OBS
+jobs/JGLOBAL_ENKF_UPDATE
+jobs/JGLOBAL_NCEPPOST
+jobs/JGLOBAL_POST_MANAGER
+scripts/exemcsfc_global_sfc_prep.sh.ecf
+scripts/exgdas_gldas.sh.ecf
+scripts/exgdas_nceppost.sh.ecf
+scripts/exgdas_vrfminmon.sh.ecf
+scripts/exgdas_vrfyozn.sh.ecf
+scripts/exgdas_vrfyrad.sh.ecf
+scripts/exgfs_nceppost.sh.ecf
+scripts/exgfs_vrfminmon.sh.ecf
+scripts/exgfs_wafs_blending.sh.ecf
+scripts/exgfs_wafs_gcip.sh.ecf
+scripts/exgfs_wafs_grib.sh.ecf
+scripts/exgfs_wafs_grib2.sh.ecf
+scripts/exglobal_analcalc_fv3gfs.sh.ecf
+scripts/exglobal_analdiag_fv3gfs.sh.ecf
+scripts/exglobal_analysis_fv3gfs.sh.ecf
+scripts/exglobal_enkf_chgres_fv3gfs.sh.ecf
+scripts/exglobal_enkf_fcst_fv3gfs.sh.ecf
+scripts/exglobal_enkf_innovate_obs_fv3gfs.sh.ecf
+scripts/exglobal_enkf_post_fv3gfs.sh.ecf
+scripts/exglobal_enkf_recenter_fv3gfs.sh.ecf
+scripts/exglobal_enkf_surface_fv3gfs.sh.ecf
+scripts/exglobal_enkf_update_fv3gfs.sh.ecf
+scripts/exglobal_innovate_obs_fv3gfs.sh.ecf
+scripts/exglobal_pmgr.sh.ecf
+ush/calcanl_gfs.py
+ush/calcinc_gfs.py
+ush/emcsfc_ice_blend.sh
+ush/emcsfc_snow.sh
+ush/fix_precip.sh
+ush/fv3gfs_chgres.sh
+ush/fv3gfs_downstream_nems.sh
+ush/fv3gfs_driver_grid.sh
+ush/fv3gfs_dwn_nems.sh
+ush/fv3gfs_filter_topo.sh
+ush/fv3gfs_make_grid.sh
+ush/fv3gfs_make_orog.sh
+ush/getncdimlen
+ush/gfs_nceppost.sh
+ush/gfs_transfer.sh
+ush/gldas_archive.sh
+ush/gldas_forcing.sh
+ush/gldas_get_data.sh
+ush/gldas_liscrd.sh
+ush/gldas_post.sh
+ush/gldas_process_data.sh
+ush/global_chgres.sh
+ush/global_chgres_driver.sh
+ush/global_cycle.sh
+ush/global_cycle_driver.sh
+ush/gsi_utils.py
+ush/link_crtm_fix.sh
+ush/minmon_xtrct_costs.pl
+ush/minmon_xtrct_gnorms.pl
+ush/minmon_xtrct_reduct.pl
+ush/mkwfsgbl.sh
+ush/mod_icec.sh
+ush/ozn_xtrct.sh
+ush/radmon_ck_stdout.sh
+ush/radmon_err_rpt.sh
+ush/radmon_verf_angle.sh
+ush/radmon_verf_bcoef.sh
+ush/radmon_verf_bcor.sh
+ush/radmon_verf_time.sh
+ush/trim_rh.sh
+ush/wafs_blending.sh
+ush/wafs_intdsk.sh
+util/sub_slurm
+util/sub_wcoss_c
+util/sub_wcoss_d

FV3GFSwfm/rt_ccpp-chem/config.anal

@@ -0,0 +1,126 @@
+#!/bin/ksh -x
+
+########## config.anal ##########
+# Analysis specific
+
+echo "BEGIN: config.anal"
+
+# Get task specific resources
+. $EXPDIR/config.resources anal
+
+if [ $DONST = "YES" ]; then
+    . $EXPDIR/config.nsst
+fi
+
+if [[ "$CDUMP" = "gfs" ]] ; then
+    export USE_RADSTAT="NO" # This can be only used when bias correction is not-zero.
+    export GENDIAG="NO"
+    export SETUP='diag_rad=.false.,diag_pcp=.false.,diag_conv=.false.,diag_ozone=.false.,write_diag(3)=.false.,niter(2)=100,'
+    export DIAG_TARBALL="NO"
+fi
+
+export ANALYSISSH="$HOMEgsi/scripts/exglobal_analysis_fv3gfs.sh.ecf"
+export npe_gsi=$npe_anal
+
+# Set parameters specific to L127
+if [ $LEVS = "128" ]; then
+    export GRIDOPTS="nlayers(63)=1,nlayers(64)=1,"
+    export SETUP="gpstop=55,nsig_ext=56,$SETUP"
+fi
+
+# Set namelist option for LETKF
+export lobsdiag_forenkf=".false."  # anal does not need to write out jacobians
+                                   # set to .true. in config.eobs and config.eupd
+
+if [ $OUTPUT_FILE = "nemsio" ]; then
+    export DO_CALC_INCREMENT="YES"
+    export DO_CALC_ANALYSIS="NO"
+fi
+
+# Do not process the following datasets
+export GSNDBF=${GSNDBF:-/dev/null}
+export AMSREBF=${AMSREBF:-/dev/null}
+export SSMITBF=${SSMITBF:-/dev/null}
+export AMSR2BF=${AMSR2BF:-/dev/null}
+
+
+# Use experimental dumps in GFS v16 parallels
+export ABIBF="/dev/null"
+if [[ "$CDATE" -ge "2019022800" ]] ; then
+    export ABIBF="$DMPDIR/${CDUMP}x.${PDY}/${cyc}/${CDUMP}.t${cyc}z.gsrcsr.tm00.bufr_d"
+    if [[ "$CDATE" -ge "2019111000" && "$CDATE" -le "2020052612" ]]; then
+	export ABIBF="$DMPDIR/${CDUMP}y.${PDY}/${cyc}/${CDUMP}.t${cyc}z.gsrcsr.tm00.bufr_d"
+    fi
+fi
+
+export AHIBF="/dev/null"
+if [[ "$CDATE" -ge "2019042300" ]]; then
+    export AHIBF="$DMPDIR/${CDUMP}x.${PDY}/${cyc}/${CDUMP}.t${cyc}z.ahicsr.tm00.bufr_d"
+fi
+
+
+# Adjust data usage for GFS v16 parallels
+#
+#   NOTE:  Remember to set PRVT in config.prep as OBERROR is set below
+#
+# Set default values
+export CONVINFO=$FIXgsi/global_convinfo.txt
+export OZINFO=$FIXgsi/global_ozinfo.txt
+export SATINFO=$FIXgsi/global_satinfo.txt
+export OBERROR=$FIXgsi/prepobs_errtable.global
+
+
+# Set convinfo and prepobs.errtable.global for start of GFS v16 parallels
+if [[ "$CDATE" -ge "2019021900" && "$CDATE" -lt "2019110706" ]]; then
+    export CONVINFO=$FIXgsi/gfsv16_historical/global_convinfo.txt.2019021900
+    export OBERROR=$FIXgsi/gfsv16_historical/prepobs_errtable.global.2019021900
+fi
+
+# Place GOES-15 AMVs in monitor, assimilate GOES-17 AMVs, assimilate KOMPSAT-5 gps
+if [[ "$CDATE" -ge "2019110706" && "$CDATE" -lt "2020040718" ]]; then
+    export CONVINFO=$FIXgsi/gfsv16_historical/global_convinfo.txt.2019110706
+    export OBERROR=$FIXgsi/gfsv16_historical/prepobs_errtable.global.2019110706
+fi
+
+# Assimilate 135 (T) & 235 (uv) Canadian AMDAR observations
+if [[ "$CDATE" -ge "2020040718" && "$CDATE" -lt "2020052612" ]]; then
+    export CONVINFO=$FIXgsi/gfsv16_historical/global_convinfo.txt.2020040718
+fi
+
+# NOTE:
+#   As of 2020052612, gfsv16_historical/global_convinfo.txt.2020052612 is
+#   identical to ../global_convinfo.txt.  Thus, the logic below is not
+#   needed at this time.
+# Assimilate COSMIC-2 GPS
+##if [[ "$CDATE" -ge "2020052612" && "$CDATE" -lt "YYYYMMDDHH" ]]; then
+##    export CONVINFO=$FIXgsi/gfsv16_historical/global_convinfo.txt.2020052612
+##fi
+
+
+# Turn off assmilation of OMPS during period of bad data
+if [[ "$CDATE" -ge "2020011600" && "$CDATE" -lt "2020011806" ]]; then
+    export OZINFO=$FIXgsi/gfsv16_historical/global_ozinfo.txt.2020011600
+fi
+
+
+# Set satinfo for start of GFS v16 parallels
+if [[ "$CDATE" -ge "2019021900" && "$CDATE" -lt "2019110706" ]]; then
+    export SATINFO=$FIXgsi/gfsv16_historical/global_satinfo.txt.2019021900
+fi
+
+# Turn on assimilation of Metop-C AMSUA and MHS
+if [[ "$CDATE" -ge "2019110706" && "$CDATE" -lt "2020022012" ]]; then
+    export SATINFO=$FIXgsi/gfsv16_historical/global_satinfo.txt.2019110706
+fi
+
+# NOTE:  
+#   As of 2020022012, gfsv16_historical/global_satinfo.txt.2020022012 is
+#   identical to ../global_satinfo.txt.  Thus, the logic below is not
+#   needed at this time
+#
+# Turn off assmilation of all Metop-A MHS
+##  if [[ "$CDATE" -ge "2020022012" && "$CDATE" -lt "YYYYMMDDHH" ]]; then
+##      export SATINFO=$FIXgsi/gfsv16_historical/global_satinfo.txt.2020022012
+##  fi
+
+echo "END: config.anal"

FV3GFSwfm/rt_ccpp-chem/config.analcalc

@@ -0,0 +1,13 @@
+#!/bin/ksh -x
+
+########## config.analcalc ##########
+# GFS post-anal specific (non-diag)
+
+echo "BEGIN: config.analcalc"
+
+# Get task specific resources
+. $EXPDIR/config.resources analcalc
+
+export ANALCALCSH=$HOMEgsi/scripts/exglobal_analcalc_fv3gfs.sh.ecf
+
+echo "END: config.analcalc"

FV3GFSwfm/rt_ccpp-chem/config.analdiag

@@ -0,0 +1,13 @@
+#!/bin/ksh -x
+
+########## config.analdiag ##########
+# GFS post-anal specific (diag)
+
+echo "BEGIN: config.analdiag"
+
+# Get task specific resources
+. $EXPDIR/config.resources analdiag
+
+export ANALDIAGSH=$HOMEgsi/scripts/exglobal_analdiag_fv3gfs.sh.ecf
+
+echo "END: config.analdiag"

FV3GFSwfm/rt_ccpp-chem/config.arch

@@ -0,0 +1,25 @@
+#!/bin/ksh -x
+
+########## config.arch ##########
+# Archive specific
+
+echo "BEGIN: config.arch"
+
+# Get task specific resources
+. $EXPDIR/config.resources arch
+
+#--online archive of nemsio files for fit2obs verification
+export FITSARC="YES"
+export FHMAX_FITS=132
+[[ "$FHMAX_FITS" -gt "$FHMAX_GFS" ]] && export FHMAX_FITS=$FHMAX_GFS
+
+#--starting and ending hours of previous cycles to be removed from rotating directory
+export RMOLDSTD=144
+export RMOLDEND=24
+
+#--keep forcing data for running gldas step
+if [[ "$DO_GLDAS" == "YES" && "$CDUMP" == "gdas" ]]; then
+     [[ $RMOLDSTD -lt 144 ]] && export RMOLDSTD=144   
+fi
+
+echo "END: config.arch"

FV3GFSwfm/rt_ccpp-chem/config.awips

@@ -0,0 +1,17 @@
+#!/bin/ksh -x
+
+########## config.awips ##########
+# GFS awips step specific
+
+echo "BEGIN: config.awips"
+
+# Get task specific resources
+. $EXPDIR/config.resources awips
+
+export AWIPS20SH=$HOMEgfs/jobs/JGFS_AWIPS_20KM_1P0DEG
+export AWIPSG2SH=$HOMEgfs/jobs/JGFS_AWIPS_G2
+
+# No. of concurrent awips jobs
+export NAWIPSGRP=42
+
+echo "END: config.awips"