Merge branch 'develop' into cpldg_tests

Fixes ufs-community#1016.

.github/PULL_REQUEST_TEMPLATE

@@ -19,6 +19,7 @@ If there are changes to the build or source code, the tests below must be conduc
 - [ ] Compile branch on all Tier 1 machines using Intel (Orion, Jet, Hera, Hercules and WCOSS2).
 - [ ] Compile branch on Hera using GNU.
 - [ ] Compile branch in 'Debug' mode on WCOSS2.
+- [ ] Compile with Doxygen on any machine with no errors.
 - [ ] Run unit tests locally on any Tier 1 machine.
 - [ ] Run relevant consistency tests locally on all Tier 1 machines.
 
@@ -34,6 +35,10 @@ Add any links to pending PRs that are required prior to merging this PR. For exa
 ufs-community/UFS_UTILS/pull/<pr_number>
 
 ## DOCUMENTATION:
+All new and updated source code must be documented with Doxygen.
+
+- [ ] Doxygen is updated.
+
 If this PR is contributing new capabilities that need to be documented, please also include updates to the RST files in the docs/source directory as supporting material.
 
 ## ISSUE: 

reg_tests/global_cycle/C192.gsi_lndincsoilnoahmp.sh

@@ -37,8 +37,9 @@ export DONST="NO"
 export use_ufo=.true.
 
 export DO_SFCCYCLE=".FALSE." 
-export DO_LNDINC=".TRUE." 
-export DO_SOI_INC_GSI=".true."
+export GCYCLE_DO_SOILINCR=".true."
+export GCYCLE_INTERP_LANDINCR=".true."
+export LSOIL_INCR=3
 
 export VERBOSE=YES
 export CYCLVARS=FSNOL=-2.,FSNOS=99999.,
@@ -86,7 +87,7 @@ if [ $test_failed -ne 0 ]; then
   echo "<<< C192 GSI based LANDINC SOIL-NOAHMP CYCLE TEST FAILED. >>>"
   echo "**********************************************"
   if [ "$UPDATE_BASELINE" = "TRUE" ]; then
-    $HOMEgfs/reg_tests/update_baseline.sh $HOMEreg "c192.lndincsoilnoahmp" $commit_num
+    $HOMEgfs/reg_tests/update_baseline.sh $HOMEreg "c192.gsi_lndincsoilnoahmp" $commit_num
   fi
 else
   echo

reg_tests/global_cycle/C192.gsitile_lndincsoilnoahmp.sh

@@ -0,0 +1,87 @@
+#!/bin/bash
+
+#------------------------------------------------------------------
+# Run global_cycle for a C192 case to test the ingest and
+# application of soil moisture and temperature increments
+# from the GSI, into Noah-MP restarts.
+# Compare output to a baseline set of files using the 'nccmp' 
+# utility.
+#------------------------------------------------------------------
+
+set -x
+
+NCCMP=${NCCMP:-$(which nccmp)}
+
+export MAX_TASKS_CY=6
+
+export HOMEgfs=$NWPROD
+
+export FIXgfs=$HOMEreg/fix
+
+export CYCLEXEC=$HOMEgfs/exec/global_cycle
+
+export CDATE=2019073000
+export FHOUR=00
+export DELTSFC=6
+
+export CASE=C192
+export OCNRES=99999
+
+export COMIN=$HOMEreg/input_data_noahmp
+
+export JCAP=1534
+export LONB=3072
+export LATB=1536
+
+export DONST="NO"
+export use_ufo=.true.
+
+export DO_SFCCYCLE=".FALSE." 
+export GCYCLE_DO_SOILINCR=".true."
+export GCYCLE_INTERP_LANDINCR=".false."
+export LSOIL_INCR=3
+
+export VERBOSE=YES
+export CYCLVARS=FSNOL=-2.,FSNOS=99999.,
+
+$HOMEgfs/ush/global_cycle_driver.sh
+
+iret=$?
+if [ $iret -ne 0 ]; then
+  set +x
+  echo "<<< C192 GSI-TILE based LANDINC SOIL NOAHMP CYCLE TEST FAILED. >>>"
+  exit $iret
+fi
+
+test_failed=0
+
+cd $DATA
+for files in *tile*.nc
+do
+  if [ -f $files ]; then
+    echo CHECK $files
+    $NCCMP -dmfqS $files $HOMEreg/baseline_data/c192.gsitile_lndincsoilnoahmp/$files
+    iret=$?
+    if [ $iret -ne 0 ]; then
+      test_failed=1
+    fi
+  fi
+done
+
+set +x
+if [ $test_failed -ne 0 ]; then
+  echo
+  echo "**********************************************"
+  echo "<<< C192 GSI-TILE based LANDINC SOIL-NOAHMP CYCLE TEST FAILED. >>>"
+  echo "**********************************************"
+  if [ "$UPDATE_BASELINE" = "TRUE" ]; then
+    $HOMEgfs/reg_tests/update_baseline.sh $HOMEreg "c192.gsitile_lndincsoilnoahmp" $commit_num
+  fi
+else
+  echo
+  echo "*****************************************"
+  echo "<<< C192 GSI-TILE based LANDINC SOIL-NOAHMP CYCLE TEST PASSED. >>>"
+  echo "*****************************************"
+fi
+
+exit

reg_tests/global_cycle/C192.jedi_lndincsoilnoahmp.sh

@@ -39,8 +39,10 @@ export DONST="NO"
 export use_ufo=.true.
 
 export DO_SFCCYCLE=".FALSE." 
-export DO_LNDINC=".TRUE." 
-export DO_SOI_INC_JEDI=".true."
+export GCYCLE_DO_SOILINCR=".true."
+export GCYCLE_INTERP_LANDINCR=".false."
+export SOILINCR_FNAME="soil_sfcincr_jedi"
+export LSOIL_INCR=3
 
 export VERBOSE=YES
 export CYCLVARS=FSNOL=-2.,FSNOS=99999.,

reg_tests/global_cycle/C768.lndincsnow.sh

@@ -31,8 +31,8 @@ export FNSNOA=$COMIN/gdas.t00z.snogrb_t1534.3072.1536
 export FNACNA=$COMIN/gdas.t00z.seaice.5min.blend.grb
 export NST_FILE=$COMIN/gdas.t00z.dtfanl.nc
 
-export DO_SNO_INC_JEDI=.true. # must be lower-case.
-export DO_SOI_INC_JEDI=.false.
+export GCYCLE_DO_SNOWINCR=.true. # must be lower-case.
+export GCYCLE_INTERP_LANDINCR=.false.
 export JCAP=1534
 export LONB=3072
 export LATB=1536
@@ -41,7 +41,6 @@ export DONST="NO"
 export use_ufo=.true.
 
 export DO_SFCCYCLE=".FALSE." 
-export DO_LNDINC=".TRUE." 
 
 export VERBOSE=YES
 export CYCLVARS=FSNOL=99999.,FSNOS=99999.,

reg_tests/global_cycle/driver.hera.sh

@@ -85,10 +85,16 @@ export COMOUT=$DATA
 TEST5=$(sbatch --parsable --ntasks-per-node=6 --nodes=1 -t 0:05:00 -A $PROJECT_CODE -q $QUEUE -J c192.jedi_lndincsoilnoahmp \
      -o $LOG_FILE -e $LOG_FILE ./C192.jedi_lndincsoilnoahmp.sh)
 
+LOG_FILE=consistency.log06
+export DATA="${DATA_DIR}/test6"
+export COMOUT=$DATA
+TEST6=$(sbatch --parsable --ntasks-per-node=6 --nodes=1 -t 0:05:00 -A $PROJECT_CODE -q $QUEUE -J C192.gsitile_lndincsoilnoahmp \
+     -o $LOG_FILE -e $LOG_FILE ./C192.gsitile_lndincsoilnoahmp.sh)
+
 LOG_FILE=consistency.log
 sbatch --nodes=1 -t 0:01:00 -A $PROJECT_CODE -J chgres_summary -o $LOG_FILE -e $LOG_FILE \
       --open-mode=append -q $QUEUE -d\
-      afterok:$TEST1:$TEST2:$TEST3:$TEST4:$TEST5 << EOF
+      afterok:$TEST1:$TEST2:$TEST3:$TEST4:$TEST5:$TEST6 << EOF
 #!/bin/bash
 grep -a '<<<' ${LOG_FILE}*  > summary.log
 EOF

reg_tests/global_cycle/driver.hercules.sh

@@ -85,10 +85,16 @@ export COMOUT=$DATA
 TEST5=$(sbatch --parsable --ntasks-per-node=6 --nodes=1 -t 0:05:00 -A $PROJECT_CODE -q $QUEUE -J c192.jedi_lndincsoilnoahmp \
      -o $LOG_FILE -e $LOG_FILE ./C192.jedi_lndincsoilnoahmp.sh)
 
+LOG_FILE=consistency.log06
+export DATA="${DATA_DIR}/test6"
+export COMOUT=$DATA
+TEST6=$(sbatch --parsable --ntasks-per-node=6 --nodes=1 -t 0:05:00 -A $PROJECT_CODE -q $QUEUE -J C192.gsitile_lndincsoilnoahmp \
+     -o $LOG_FILE -e $LOG_FILE ./C192.gsitile_lndincsoilnoahmp.sh)
+
 LOG_FILE=consistency.log
 sbatch --nodes=1 -t 0:01:00 -A $PROJECT_CODE -J chgres_summary -o $LOG_FILE -e $LOG_FILE \
       --open-mode=append -q $QUEUE -d\
-      afterok:$TEST1:$TEST2:$TEST3:$TEST4:$TEST5 << EOF
+      afterok:$TEST1:$TEST2:$TEST3:$TEST4:$TEST5:$TEST6 << EOF
 #!/bin/bash
 grep -a '<<<' ${LOG_FILE}*  > summary.log
 EOF

reg_tests/global_cycle/driver.jet.sh

@@ -85,10 +85,16 @@ export COMOUT=$DATA
 TEST5=$(sbatch --parsable --ntasks-per-node=6 --nodes=1 -t 0:05:00 -A $PROJECT_CODE -q $QUEUE -J c192.jedi_lndincsoilnoahmp \
      -o $LOG_FILE -e $LOG_FILE ./C192.jedi_lndincsoilnoahmp.sh)
 
+LOG_FILE=consistency.log06
+export DATA="${DATA_DIR}/test6"
+export COMOUT=$DATA
+TEST6=$(sbatch --parsable --ntasks-per-node=6 --nodes=1 -t 0:05:00 -A $PROJECT_CODE -q $QUEUE -J C192.gsitile_lndincsoilnoahmp \
+     --partition=xjet -o $LOG_FILE -e $LOG_FILE ./C192.gsitile_lndincsoilnoahmp.sh)
+
 LOG_FILE=consistency.log
 sbatch --partition=xjet --nodes=1  -t 0:01:00 -A $PROJECT_CODE -J summary -o $LOG_FILE -e $LOG_FILE \
        --open-mode=append -q $QUEUE -d\
-       afterok:$TEST1:$TEST2:$TEST3:$TEST4:$TEST5 << EOF
+       afterok:$TEST1:$TEST2:$TEST3:$TEST4:$TEST5:$TEST6 << EOF
 #!/bin/bash
 grep -a '<<<' ${LOG_FILE}* > ./summary.log
 EOF

reg_tests/global_cycle/driver.orion.sh

@@ -83,10 +83,16 @@ export COMOUT=$DATA
 TEST5=$(sbatch --parsable --ntasks-per-node=6 --nodes=1 -t 0:05:00 -A $PROJECT_CODE -q $QUEUE -J c192.jedi_lndincsoilnoahmp \
      -o $LOG_FILE -e $LOG_FILE ./C192.jedi_lndincsoilnoahmp.sh)
 
+LOG_FILE=consistency.log06
+export DATA="${DATA_DIR}/test6"
+export COMOUT=$DATA
+TEST6=$(sbatch --parsable --ntasks-per-node=6 --nodes=1 -t 0:05:00 -A $PROJECT_CODE -q $QUEUE -J C192.gsitile_lndincsoilnoahmp \
+     -o $LOG_FILE -e $LOG_FILE ./C192.gsitile_lndincsoilnoahmp.sh)
+
 LOG_FILE=consistency.log
 sbatch --nodes=1 -t 0:01:00 -A $PROJECT_CODE -J chgres_summary -o $LOG_FILE -e $LOG_FILE \
       --open-mode=append -q $QUEUE -d\
-      afterok:$TEST1:$TEST2:$TEST3:$TEST4:$TEST5 << EOF
+      afterok:$TEST1:$TEST2:$TEST3:$TEST4:$TEST5:$TEST6 << EOF
 #!/bin/bash
 grep -a '<<<' ${LOG_FILE}*  > summary.log
 EOF

reg_tests/global_cycle/driver.wcoss2.sh

@@ -86,8 +86,13 @@ export COMOUT=$DATA
 TEST5=$(qsub -V -o ${LOG_FILE}05 -e ${LOG_FILE}05 -q $QUEUE -A $PROJECT_CODE -l walltime=00:05:00 \
         -N c192.jedi_lndincsoilnoahmp -l select=1:ncpus=12:mem=8GB $PWD/C192.jedi_lndincsoilnoahmp.sh)
 
+export DATA="${DATA_DIR}/test6"
+export COMOUT=$DATA
+TEST6=$(qsub -V -o ${LOG_FILE}06 -e ${LOG_FILE}06 -q $QUEUE -A $PROJECT_CODE -l walltime=00:05:00 \
+        -N c192.gsitile_lndincsoilnoahmp -l select=1:ncpus=12:mem=8GB $PWD/C192.gsitile_lndincsoilnoahmp.sh)
+
 qsub -V -o ${LOG_FILE} -e ${LOG_FILE} -q $QUEUE -A $PROJECT_CODE -l walltime=00:01:00 \
-        -N cycle_summary -l select=1:ncpus=1:mem=100MB -W depend=afterok:$TEST1:$TEST2:$TEST3:$TEST4:$TEST5 << EOF
+        -N cycle_summary -l select=1:ncpus=1:mem=100MB -W depend=afterok:$TEST1:$TEST2:$TEST3:$TEST4:$TEST5:$TEST6 << EOF
 #!/bin/bash
 cd $reg_dir
 grep -a '<<<' ${LOG_FILE}?? | grep -v echo > summary.log