From 013c6dac7a3e063f4eba0cdc2f702de98dad9bb0 Mon Sep 17 00:00:00 2001
From: Craig Hartsough <craig.hartsough@noaa.gov>
Date: Wed, 16 Aug 2023 15:24:30 +0000
Subject: [PATCH 1/5] initial uncertainty code

---
 scripts/exregional_nonvarcldanl.sh | 6 ++++++
 ush/config_defaults.sh             | 1 +
 2 files changed, 7 insertions(+)

diff --git a/scripts/exregional_nonvarcldanl.sh b/scripts/exregional_nonvarcldanl.sh
index aa653627b..f32dac209 100755
--- a/scripts/exregional_nonvarcldanl.sh
+++ b/scripts/exregional_nonvarcldanl.sh
@@ -165,6 +165,9 @@ else
     bkpath=${cycle_dir}${slash_ensmem_subdir}/fcst_fv3lam${cycle_tag}/INPUT
 fi
 
+# Copy analysis fields into uncertainties
+cp_vrfy ${bkpath}/fv_tracer.res.tile1.nc  ${bkpath}/fv_tracer.unc.tile1.nc
+
 n_iolayouty=$(($IO_LAYOUT_Y-1))
 list_iolayout=$(seq 0 $n_iolayouty)
 
@@ -175,6 +178,7 @@ if [ -r "${bkpath}/coupler.res" ]; then # Use background from warm restart
   if [ "${IO_LAYOUT_Y}" == "1" ]; then
     ln_vrfy -s ${bkpath}/fv_core.res.tile1.nc         fv3_dynvars
     ln_vrfy -s ${bkpath}/fv_tracer.res.tile1.nc       fv3_tracer
+    ln_vrfy -s ${bkpath}/fv_tracer.unc.tile1.nc       fv3_tracer_unc
     ln_vrfy -s ${bkpath}/sfc_data.nc                  fv3_sfcdata
     ln_vrfy -s ${bkpath}/phy_data.nc                  fv3_phydata
   else
@@ -183,6 +187,7 @@ if [ -r "${bkpath}/coupler.res" ]; then # Use background from warm restart
       iii=$(printf %4.4i $ii)
       ln_vrfy -s ${bkpath}/fv_core.res.tile1.nc.${iii}         fv3_dynvars.${iii}
       ln_vrfy -s ${bkpath}/fv_tracer.res.tile1.nc.${iii}       fv3_tracer.${iii}
+      ln_vrfy -s ${bkpath}/fv_tracer.unc.tile1.nc.${iii}       fv3_tracer_unc.${iii}
       ln_vrfy -s ${bkpath}/sfc_data.nc.${iii}                  fv3_sfcdata.${iii}
       ln_vrfy -s ${bkpath}/phy_data.nc.${iii}                  fv3_phydata.${iii}
       ln_vrfy -s ${gridspec_dir}/fv3_grid_spec.${iii}          fv3_grid_spec.${iii}
@@ -312,6 +317,7 @@ cat << EOF > gsiparm.anl
    i_T_Q_adjust=${i_T_Q_adjust},
    l_rtma3d=${l_rtma3d},
    i_precip_vertical_check=${i_precip_vertical_check},
+   i_uncertainty=${i_uncertainty},
  /
 EOF
 
diff --git a/ush/config_defaults.sh b/ush/config_defaults.sh
index f5c0308e9..18760565a 100644
--- a/ush/config_defaults.sh
+++ b/ush/config_defaults.sh
@@ -715,6 +715,7 @@ i_use_2mT4B=0
 i_T_Q_adjust=1
 l_rtma3d=.false.
 i_precip_vertical_check=0
+i_uncertainty=0
 #  &CHEM 
 laeroana_fv3smoke=.false.
 berror_fv3_cmaq_regional=.false.

From 2dab9e8fcdfcba6eaae33c7ce564cb982968f23d Mon Sep 17 00:00:00 2001
From: Craig Hartsough <craig.hartsough@noaa.gov>
Date: Tue, 22 Aug 2023 18:54:46 +0000
Subject: [PATCH 2/5] change flag to logical, clean commented-out lines

---
 scripts/exregional_nonvarcldanl.sh | 7 +++++--
 ush/config_defaults.sh             | 2 +-
 2 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/scripts/exregional_nonvarcldanl.sh b/scripts/exregional_nonvarcldanl.sh
index f32dac209..0bf2aa86f 100755
--- a/scripts/exregional_nonvarcldanl.sh
+++ b/scripts/exregional_nonvarcldanl.sh
@@ -165,8 +165,11 @@ else
     bkpath=${cycle_dir}${slash_ensmem_subdir}/fcst_fv3lam${cycle_tag}/INPUT
 fi
 
-# Copy analysis fields into uncertainties
-cp_vrfy ${bkpath}/fv_tracer.res.tile1.nc  ${bkpath}/fv_tracer.unc.tile1.nc
+if [ ${i_uncertainty} == ".true." ]; then
+  # Copy analysis fields into uncertainties - data will be overwritten
+  echo "EXREGIONAL_NONVARCLDANL.SH: copy tracer file into uncertainty file "
+  cp_vrfy ${bkpath}/fv_tracer.res.tile1.nc  ${bkpath}/fv_tracer.unc.tile1.nc
+fi
 
 n_iolayouty=$(($IO_LAYOUT_Y-1))
 list_iolayout=$(seq 0 $n_iolayouty)
diff --git a/ush/config_defaults.sh b/ush/config_defaults.sh
index 18760565a..12fe91ec4 100644
--- a/ush/config_defaults.sh
+++ b/ush/config_defaults.sh
@@ -715,7 +715,7 @@ i_use_2mT4B=0
 i_T_Q_adjust=1
 l_rtma3d=.false.
 i_precip_vertical_check=0
-i_uncertainty=0
+i_uncertainty=.false.
 #  &CHEM 
 laeroana_fv3smoke=.false.
 berror_fv3_cmaq_regional=.false.

From 1b2a89eeb59ebc1b3e206c7816e6a7ef6f38356f Mon Sep 17 00:00:00 2001
From: Craig Hartsough <craig.hartsough@noaa.gov>
Date: Wed, 23 Aug 2023 18:52:13 +0000
Subject: [PATCH 3/5] change uncertainty flag, now a logical, to l_uncertainty

---
 scripts/exregional_nonvarcldanl.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/scripts/exregional_nonvarcldanl.sh b/scripts/exregional_nonvarcldanl.sh
index 0bf2aa86f..b38262089 100755
--- a/scripts/exregional_nonvarcldanl.sh
+++ b/scripts/exregional_nonvarcldanl.sh
@@ -165,7 +165,7 @@ else
     bkpath=${cycle_dir}${slash_ensmem_subdir}/fcst_fv3lam${cycle_tag}/INPUT
 fi
 
-if [ ${i_uncertainty} == ".true." ]; then
+if [ ${l_uncertainty} == ".true." ]; then
   # Copy analysis fields into uncertainties - data will be overwritten
   echo "EXREGIONAL_NONVARCLDANL.SH: copy tracer file into uncertainty file "
   cp_vrfy ${bkpath}/fv_tracer.res.tile1.nc  ${bkpath}/fv_tracer.unc.tile1.nc
@@ -320,7 +320,7 @@ cat << EOF > gsiparm.anl
    i_T_Q_adjust=${i_T_Q_adjust},
    l_rtma3d=${l_rtma3d},
    i_precip_vertical_check=${i_precip_vertical_check},
-   i_uncertainty=${i_uncertainty},
+   l_uncertainty=${l_uncertainty},
  /
 EOF
 

From 538332831e9e00111e89f71e4b58a42caa9aee1a Mon Sep 17 00:00:00 2001
From: Craig Hartsough <craig.hartsough@noaa.gov>
Date: Wed, 23 Aug 2023 19:00:44 +0000
Subject: [PATCH 4/5] change to l_uncertainty in config_defaults

---
 ush/config_defaults.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ush/config_defaults.sh b/ush/config_defaults.sh
index 12fe91ec4..a5ebeb39a 100644
--- a/ush/config_defaults.sh
+++ b/ush/config_defaults.sh
@@ -715,7 +715,7 @@ i_use_2mT4B=0
 i_T_Q_adjust=1
 l_rtma3d=.false.
 i_precip_vertical_check=0
-i_uncertainty=.false.
+l_uncertainty=.false.
 #  &CHEM 
 laeroana_fv3smoke=.false.
 berror_fv3_cmaq_regional=.false.

From 1bdf04557929d325891c711ab5ff16c804f61827 Mon Sep 17 00:00:00 2001
From: Craig Hartsough <craig.hartsough@noaa.gov>
Date: Thu, 24 Aug 2023 13:33:05 +0000
Subject: [PATCH 5/5] change flag name to be more specific, l_cld_uncertainty

---
 scripts/exregional_nonvarcldanl.sh | 4 ++--
 ush/config_defaults.sh             | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/scripts/exregional_nonvarcldanl.sh b/scripts/exregional_nonvarcldanl.sh
index b38262089..70d043e66 100755
--- a/scripts/exregional_nonvarcldanl.sh
+++ b/scripts/exregional_nonvarcldanl.sh
@@ -165,7 +165,7 @@ else
     bkpath=${cycle_dir}${slash_ensmem_subdir}/fcst_fv3lam${cycle_tag}/INPUT
 fi
 
-if [ ${l_uncertainty} == ".true." ]; then
+if [ ${l_cld_uncertainty} == ".true." ]; then
   # Copy analysis fields into uncertainties - data will be overwritten
   echo "EXREGIONAL_NONVARCLDANL.SH: copy tracer file into uncertainty file "
   cp_vrfy ${bkpath}/fv_tracer.res.tile1.nc  ${bkpath}/fv_tracer.unc.tile1.nc
@@ -320,7 +320,7 @@ cat << EOF > gsiparm.anl
    i_T_Q_adjust=${i_T_Q_adjust},
    l_rtma3d=${l_rtma3d},
    i_precip_vertical_check=${i_precip_vertical_check},
-   l_uncertainty=${l_uncertainty},
+   l_cld_uncertainty=${l_cld_uncertainty},
  /
 EOF
 
diff --git a/ush/config_defaults.sh b/ush/config_defaults.sh
index a5ebeb39a..b0a9d9552 100644
--- a/ush/config_defaults.sh
+++ b/ush/config_defaults.sh
@@ -715,7 +715,7 @@ i_use_2mT4B=0
 i_T_Q_adjust=1
 l_rtma3d=.false.
 i_precip_vertical_check=0
-l_uncertainty=.false.
+l_cld_uncertainty=.false.
 #  &CHEM 
 laeroana_fv3smoke=.false.
 berror_fv3_cmaq_regional=.false.