Merge pull request NOAA-EMC#14 from jkhender/feature/chem

Feature/chem

Externals.cfg

@@ -2,11 +2,18 @@
 
 [FV3GFS]
 tag = GFS.v16.0.10
-local_path = sorc/fv3gfs.fd
+local_path = sorc/fv3gfs_emc.fd
 repo_url = https://github.com/ufs-community/ufs-weather-model.git
 protocol = git
 required = True
 
+[CCPPFV3GFS]
+hash = 433fc66b
+local_path = sorc/fv3gfs_ccpp.fd
+repo_url = https://github.com/haiqinli/ufs-weather-model
+protocol = git
+required = True
+
 [GSI]
 branch = release/gfsda.v16.0.0
 local_path = sorc/gsi.fd

INFO

@@ -0,0 +1,28 @@
+============
+Oct 20, 2020
+============
+updated to 18May2020 gsd/develop-chem branch from Haiqin Li's fork, 433fc66
+   708b8d5e5e044860bfc409c22524eb9fb8b25ff3 FMS (2019.01)
+    2a28f9167e5ad7082df07fd6fe5078695b12719f FV3 (remotes/origin/gsd/develop-chem)
+     e53a24be1bee834a14f5f85ef5d8d18f431d6b16 atmos_cubed_sphere (heads/gsd/develop)
+     c0faa3a31fa10a9740ab94d75dd548565e0c8c08 ccpp/framework (ccpp_transition_to_vlab_master_20190705-81-gc0faa3a)
+     cd71dd3483d11fb446563be8b764f90f150c52dd ccpp/physics (ccpp_transition_to_vlab_master_20190705-171-gcd71dd3)
+   8248a782d7193d41b773f6d90611c936e11e3c7f NEMS (8248a78)
+   f6ebf95ff3bfa0bcbde1e5dbddf5a3e7760c6965 WW3 (6.07.1-27-gf6ebf95f)
+   1745422af76d830757cd6035b6ea101e92b4cac1 stochastic_physics (GFS_v16.0.0)
+
+
+GSD changes:
+   jobs/rocoto/aeroic.sh
+   jobs/rocoto/arch_gsd.sh
+   jobs/rocoto/getic_gsd_fv3gfs.sh
+   jobs/rocoto/getic_gsd_gfs.sh
+
+   parm/parm_fv3diag/diag_table_da_gsd
+   parm/parm_fv3diag/diag_table_gsd
+   parm/parm_fv3diag/diag_table_gsd_ruc
+   parm/parm_fv3diag/field_table_gsd
+
+   sorc/aeroic.fd
+   ush/rocoto/setup_workflow_fcstonly_gsd.py
+

jobs/rocoto/aeroic.sh

@@ -0,0 +1,79 @@
+#!/bin/bash
+
+###############################################################
+# Source relevant configs
+configs="base"
+for config in $configs; do
+    . $EXPDIR/config.${config}
+    status=$?
+    [[ $status -ne 0 ]] && exit $status
+done
+
+# initialize
+AERO_DIR=${HOMEgfs}/sorc/aeroconv.fd
+module purge
+module load intel/18.0.5.274
+module load hdf5/1.10.5
+module load netcdf/4.7.0
+module load grib_api/1.26.1
+module use /contrib/anaconda/modulefiles
+module load anaconda/2.3.0
+module load nco/4.7.0
+module load ncl/6.5.0
+export LD_PRELOAD=$AERO_DIR/thirdparty/lib/libjpeg.so
+export PATH=$AERO_DIR/thirdparty/bin:$PATH
+export LD_LIBRARY_PATH=$AERO_DIR/thirdparty/lib:$AERO_DIR/thirdparty/lib64:$LD_LIBRARY_PATH
+export PYTHONPATH=$AERO_DIR/thirdparty/lib/python2.7/site-packages:$PYTHONPATH
+
+module use -a /scratch1/BMC/gmtb/software/modulefiles/intel-18.0.5.274/impi-2018.0.4
+module load cdo/1.7.2
+
+# set case from environment variable passed in!!
+echo
+echo "FIXfv3 = $FIXfv3"
+echo "CDATE = $CDATE"
+echo "AERO_DIR = $AERO_DIR"
+echo "AEROCASE = $AEROCASE"
+echo "FV3ICS_DIR = $FV3ICS_DIR"
+echo
+
+# Temporary runtime directory
+export DATA="$DATAROOT/aerofv3ic$$"
+[[ -d $DATA ]] && rm -rf $DATA
+mkdir -p $DATA/INPUT
+cd $DATA
+echo entering $DATA....
+
+# link files
+ln -sf ${AERO_DIR}/thirdparty 
+ln -sf ${FV3ICS_DIR}/gfs_ctrl.nc INPUT       
+ln -sf ${FV3ICS_DIR}/gfs_data.tile1.nc INPUT 
+ln -sf ${FV3ICS_DIR}/gfs_data.tile2.nc INPUT 
+ln -sf ${FV3ICS_DIR}/gfs_data.tile3.nc INPUT 
+ln -sf ${FV3ICS_DIR}/gfs_data.tile4.nc INPUT 
+ln -sf ${FV3ICS_DIR}/gfs_data.tile5.nc INPUT 
+ln -sf ${FV3ICS_DIR}/gfs_data.tile6.nc INPUT 
+ln -sf ${FIXfv3}/${AEROCASE}/${AEROCASE}_grid_spec.tile1.nc INPUT/grid_spec.tile1.nc
+ln -sf ${FIXfv3}/${AEROCASE}/${AEROCASE}_grid_spec.tile2.nc INPUT/grid_spec.tile2.nc
+ln -sf ${FIXfv3}/${AEROCASE}/${AEROCASE}_grid_spec.tile3.nc INPUT/grid_spec.tile3.nc
+ln -sf ${FIXfv3}/${AEROCASE}/${AEROCASE}_grid_spec.tile4.nc INPUT/grid_spec.tile4.nc
+ln -sf ${FIXfv3}/${AEROCASE}/${AEROCASE}_grid_spec.tile5.nc INPUT/grid_spec.tile5.nc
+ln -sf ${FIXfv3}/${AEROCASE}/${AEROCASE}_grid_spec.tile6.nc INPUT/grid_spec.tile6.nc
+ln -sf ${AERO_DIR}/INPUT/QNWFA_QNIFA_SIGMA_MONTHLY.dat.nc INPUT
+
+cp ${AERO_DIR}/int2nc_to_nggps_ic_* ./ 
+
+yyyymmdd=`echo $CDATE | cut -c1-8`
+./int2nc_to_nggps_ic_batch.sh $yyyymmdd
+
+# Move output data
+echo "copying updated files to $FV3ICS_DIR...."
+cp -p $DATA/OUTPUT/gfs*nc $FV3ICS_DIR
+status=$?
+[[ $status -ne 0 ]] && exit $status
+touch ${FV3ICS_DIR}/aero_done
+
+###############################################################
+# Force Exit out cleanly
+#if [ ${KEEPDATA:-"NO"} = "NO" ] ; then rm -rf $DATA ; fi
+#exit 0