From b7495d46de2188ee667efb7aa081b0b3b55c142b Mon Sep 17 00:00:00 2001
From: NeilBarton-NOAA <neil.barton@noaa.gov>
Date: Mon, 29 Aug 2022 07:36:33 -0500
Subject: [PATCH 1/6] 3DVAR IAU options

---
 parm/config/config.base.emc.dyn | 38 ++++++++++++++++++++-------------
 ush/parsing_namelists_FV3.sh    |  1 +
 2 files changed, 24 insertions(+), 15 deletions(-)

diff --git a/parm/config/config.base.emc.dyn b/parm/config/config.base.emc.dyn
index af18173d607..df093c86427 100755
--- a/parm/config/config.base.emc.dyn
+++ b/parm/config/config.base.emc.dyn
@@ -289,21 +289,6 @@ else
     export NETCDF_IN=".false."
 fi
 
-# IAU related parameters
-export DOIAU="YES"        # Enable 4DIAU for control with 3 increments
-export IAUFHRS="3,6,9"
-export IAU_FHROT=$(echo $IAUFHRS | cut -c1)
-export IAU_DELTHRS=6
-export IAU_OFFSET=6
-export DOIAU_ENKF=${DOIAU:-"YES"}   # Enable 4DIAU for EnKF ensemble
-export IAUFHRS_ENKF="3,6,9"
-export IAU_DELTHRS_ENKF=6
-# Check if cycle is cold starting, DOIAU off, or free-forecast mode
-if [[ "$MODE" = "cycled" && "$SDATE" = "$CDATE" && $EXP_WARM_START = ".false." ]] || [[ "$DOIAU" = "NO" ]] || [[ "$MODE" = "forecast-only" && $EXP_WARM_START = ".false." ]] ; then
-  export IAU_OFFSET=0
-  export IAU_FHROT=0
-fi
-
 # Use Jacobians in eupd and thereby remove need to run eomg
 export lobsdiag_forenkf=".true."
 
@@ -338,6 +323,7 @@ export lwrite4danl=".true."
 
 # EnKF output frequency
 if [ $DOHYBVAR = "YES" ]; then
+    export DOIAU="YES"        # Enable 4DIAU for control with 3 increments
     export FHMIN_ENKF=3
     export FHMAX_ENKF=9
     if [ $l4densvar = ".true." ]; then
@@ -346,6 +332,28 @@ if [ $DOHYBVAR = "YES" ]; then
     else
         export FHOUT_ENKF=3
     fi
+else
+  export DOIAU=${DOIAU:-"NO"}   # 3DVAR defaults to no IAU
+fi
+
+# IAU related parameters
+if [[ $DOHYBVAR == "NO" && $DOIAU == "YES"  ]]; then
+  export IAUFHRS="6"
+  export IAU_FHROT="3"
+  export IAU_FILTER_INCREMENTS=.true.
+else
+  export IAUFHRS="3,6,9" # Enable 4DIAU or control with 3 increments
+  export IAU_FHROT=$(echo $IAUFHRS | cut -c1)
+fi
+export IAU_DELTHRS=6
+export IAU_OFFSET=6
+export DOIAU_ENKF=${DOIAU:-"YES"}   # Enable 4DIAU for EnKF ensemble
+export IAUFHRS_ENKF="3,6,9"
+export IAU_DELTHRS_ENKF=6
+# Check if cycle is cold starting, DOIAU off, or free-forecast mode
+if [[ "$MODE" = "cycled" && "$SDATE" = "$CDATE" && $EXP_WARM_START = ".false." ]] || [[ "$DOIAU" = "NO" ]] || [[ "$MODE" = "forecast-only" && $EXP_WARM_START = ".false." ]] ; then
+  export IAU_OFFSET=0
+  export IAU_FHROT=0
 fi
 
 # turned on nsst in anal and/or fcst steps, and turn off rtgsst
diff --git a/ush/parsing_namelists_FV3.sh b/ush/parsing_namelists_FV3.sh
index 41fdb04f1bc..e8a1e703126 100755
--- a/ush/parsing_namelists_FV3.sh
+++ b/ush/parsing_namelists_FV3.sh
@@ -396,6 +396,7 @@ if [ $DOIAU = "YES" ]; then
   iau_delthrs  = ${IAU_DELTHRS}
   iau_inc_files= ${IAU_INC_FILES}
   iau_drymassfixer = .false.
+  iau_filter_increments = ${IAU_FILTER_INCREMENTS:-.false.}
 EOF
 fi
 

From 3b39c89c429ee3be4080ca18f895475a0f6668cf Mon Sep 17 00:00:00 2001
From: Neil Barton <103681022+NeilBarton-NOAA@users.noreply.github.com>
Date: Wed, 9 Nov 2022 12:38:27 -0500
Subject: [PATCH 2/6] Update parm/config/config.base.emc.dyn

correct

Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com>
---
 parm/config/config.base.emc.dyn | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/parm/config/config.base.emc.dyn b/parm/config/config.base.emc.dyn
index 9dc5628e011..7d049006e93 100755
--- a/parm/config/config.base.emc.dyn
+++ b/parm/config/config.base.emc.dyn
@@ -333,7 +333,7 @@ if [ $DOHYBVAR = "YES" ]; then
         export FHOUT_ENKF=3
     fi
 else
-  export DOIAU=${DOIAU:-"NO"}   # 3DVAR defaults to no IAU
+  export DOIAU="NO"   # 3DVAR defaults to no IAU
 fi
 
 # IAU related parameters

From 313987ba8e2d8a8d6021228c3aa4c65d6be9347f Mon Sep 17 00:00:00 2001
From: Neil Barton <103681022+NeilBarton-NOAA@users.noreply.github.com>
Date: Wed, 9 Nov 2022 12:39:47 -0500
Subject: [PATCH 3/6] Update parm/config/config.base.emc.dyn

Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com>
---
 parm/config/config.base.emc.dyn | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/parm/config/config.base.emc.dyn b/parm/config/config.base.emc.dyn
index 7d049006e93..900361f57d4 100755
--- a/parm/config/config.base.emc.dyn
+++ b/parm/config/config.base.emc.dyn
@@ -323,7 +323,7 @@ export lwrite4danl=".true."
 
 # EnKF output frequency
 if [ $DOHYBVAR = "YES" ]; then
-    export DOIAU="YES"        # Enable 4DIAU for control with 3 increments
+    export DOIAU="YES"
     export FHMIN_ENKF=3
     export FHMAX_ENKF=9
     if [ $l4densvar = ".true." ]; then

From c67191b2022116794153aa0135a6a712da782f58 Mon Sep 17 00:00:00 2001
From: NeilBarton-NOAA <neil.barton@noaa.gov>
Date: Wed, 9 Nov 2022 18:01:16 +0000
Subject: [PATCH 4/6] add if statement for clarity and add {} for syntax

---
 parm/config/config.base.emc.dyn | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/parm/config/config.base.emc.dyn b/parm/config/config.base.emc.dyn
index 900361f57d4..f698fbd97fd 100755
--- a/parm/config/config.base.emc.dyn
+++ b/parm/config/config.base.emc.dyn
@@ -337,7 +337,7 @@ else
 fi
 
 # IAU related parameters
-if [[ $DOHYBVAR == "NO" && $DOIAU == "YES"  ]]; then
+if [[ ${DOHYBVAR} == "NO" && ${DOIAU} == "YES"  ]]; then
   export IAUFHRS="6"
   export IAU_FHROT="3"
   export IAU_FILTER_INCREMENTS=.true.
@@ -347,11 +347,13 @@ else
 fi
 export IAU_DELTHRS=6
 export IAU_OFFSET=6
-export DOIAU_ENKF=${DOIAU:-"YES"}   # Enable 4DIAU for EnKF ensemble
-export IAUFHRS_ENKF="3,6,9"
-export IAU_DELTHRS_ENKF=6
+if [[ ${DOHYBVAR} = "YES" ]]; then
+    export DOIAU_ENKF=${DOIAU:-"YES"}   # Enable 4DIAU for EnKF ensemble
+    export IAUFHRS_ENKF="3,6,9"
+    export IAU_DELTHRS_ENKF=6
+fi
 # Check if cycle is cold starting, DOIAU off, or free-forecast mode
-if [[ "$MODE" = "cycled" && "$SDATE" = "$CDATE" && $EXP_WARM_START = ".false." ]] || [[ "$DOIAU" = "NO" ]] || [[ "$MODE" = "forecast-only" && $EXP_WARM_START = ".false." ]] ; then
+if [[ "${MODE}" = "cycled" && "${SDATE}" = "$CDATE" && ${EXP_WARM_START} = ".false." ]] || [[ "${DOIAU}" = "NO" ]] || [[ "${MODE}" = "forecast-only" && ${EXP_WARM_START} = ".false." ]] ; then
   export IAU_OFFSET=0
   export IAU_FHROT=0
 fi

From b6d8a17c8ce6fbb7567375354fd1d52d847772c7 Mon Sep 17 00:00:00 2001
From: NeilBarton-NOAA <neil.barton@noaa.gov>
Date: Thu, 1 Dec 2022 14:07:38 +0000
Subject: [PATCH 5/6] simplifying the changes for IAU and 3DVAR* " Check if
 cycle is cold starting, DOIAU off, or free-forecast mode" if statement moved
 after Hybrid variables as it's needed for new if statement

---
 parm/config/config.base.emc.dyn | 37 +++++++++++++++++----------------
 1 file changed, 19 insertions(+), 18 deletions(-)

diff --git a/parm/config/config.base.emc.dyn b/parm/config/config.base.emc.dyn
index f698fbd97fd..4032ee3e96d 100755
--- a/parm/config/config.base.emc.dyn
+++ b/parm/config/config.base.emc.dyn
@@ -289,6 +289,16 @@ else
     export NETCDF_IN=".false."
 fi
 
+# IAU related parameters
+export DOIAU="YES"        # Enable 4DIAU for control with 3 increments
+export IAUFHRS="3,6,9"
+export IAU_FHROT=$(echo $IAUFHRS | cut -c1)
+export IAU_DELTHRS=6
+export IAU_OFFSET=6
+export DOIAU_ENKF=${DOIAU:-"YES"}   # Enable 4DIAU for EnKF ensemble
+export IAUFHRS_ENKF="3,6,9"
+export IAU_DELTHRS_ENKF=6
+
 # Use Jacobians in eupd and thereby remove need to run eomg
 export lobsdiag_forenkf=".true."
 
@@ -317,43 +327,34 @@ export DO_JEDIENS="NO"
 # Hybrid related
 export DOHYBVAR="YES"
 export NMEM_ENKF=@NMEM_ENKF@
+export NMEM_EFCS=30
 export SMOOTH_ENKF="NO"
 export l4densvar=".true."
 export lwrite4danl=".true."
 
 # EnKF output frequency
 if [ $DOHYBVAR = "YES" ]; then
-    export DOIAU="YES"
     export FHMIN_ENKF=3
     export FHMAX_ENKF=9
+    export FHMAX_ENKF_GFS=120
     if [ $l4densvar = ".true." ]; then
         export FHOUT=1
         export FHOUT_ENKF=1
     else
         export FHOUT_ENKF=3
     fi
-else
-  export DOIAU="NO"   # 3DVAR defaults to no IAU
 fi
 
-# IAU related parameters
+# if 3DVAR and IAU 
 if [[ ${DOHYBVAR} == "NO" && ${DOIAU} == "YES"  ]]; then
-  export IAUFHRS="6"
-  export IAU_FHROT="3"
-  export IAU_FILTER_INCREMENTS=.true.
-else
-  export IAUFHRS="3,6,9" # Enable 4DIAU or control with 3 increments
-  export IAU_FHROT=$(echo $IAUFHRS | cut -c1)
-fi
-export IAU_DELTHRS=6
-export IAU_OFFSET=6
-if [[ ${DOHYBVAR} = "YES" ]]; then
-    export DOIAU_ENKF=${DOIAU:-"YES"}   # Enable 4DIAU for EnKF ensemble
-    export IAUFHRS_ENKF="3,6,9"
-    export IAU_DELTHRS_ENKF=6
+    export IAUFHRS="6"
+    export IAU_FHROT="3"
+    export IAU_FILTER_INCREMENTS=.true.
+    export IAUFHRS_ENKF="6"
 fi
+
 # Check if cycle is cold starting, DOIAU off, or free-forecast mode
-if [[ "${MODE}" = "cycled" && "${SDATE}" = "$CDATE" && ${EXP_WARM_START} = ".false." ]] || [[ "${DOIAU}" = "NO" ]] || [[ "${MODE}" = "forecast-only" && ${EXP_WARM_START} = ".false." ]] ; then
+if [[ "$MODE" = "cycled" && "$SDATE" = "$CDATE" && $EXP_WARM_START = ".false." ]] || [[ "$DOIAU" = "NO" ]] || [[ "$MODE" = "forecast-only" && $EXP_WARM_START = ".false." ]] ; then
   export IAU_OFFSET=0
   export IAU_FHROT=0
 fi

From b75f2d845fd0d7cc0f64e8817b3b292143044ea1 Mon Sep 17 00:00:00 2001
From: NeilBarton-NOAA <neil.barton@noaa.gov>
Date: Thu, 1 Dec 2022 19:38:33 +0000
Subject: [PATCH 6/6] adding quotes around .true. and .false.

---
 parm/config/config.base.emc.dyn | 2 +-
 ush/parsing_namelists_FV3.sh    | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/parm/config/config.base.emc.dyn b/parm/config/config.base.emc.dyn
index 4032ee3e96d..32920d62ec8 100755
--- a/parm/config/config.base.emc.dyn
+++ b/parm/config/config.base.emc.dyn
@@ -349,7 +349,7 @@ fi
 if [[ ${DOHYBVAR} == "NO" && ${DOIAU} == "YES"  ]]; then
     export IAUFHRS="6"
     export IAU_FHROT="3"
-    export IAU_FILTER_INCREMENTS=.true.
+    export IAU_FILTER_INCREMENTS=".true."
     export IAUFHRS_ENKF="6"
 fi
 
diff --git a/ush/parsing_namelists_FV3.sh b/ush/parsing_namelists_FV3.sh
index e8a1e703126..c9dc9cd1bcf 100755
--- a/ush/parsing_namelists_FV3.sh
+++ b/ush/parsing_namelists_FV3.sh
@@ -396,7 +396,7 @@ if [ $DOIAU = "YES" ]; then
   iau_delthrs  = ${IAU_DELTHRS}
   iau_inc_files= ${IAU_INC_FILES}
   iau_drymassfixer = .false.
-  iau_filter_increments = ${IAU_FILTER_INCREMENTS:-.false.}
+  iau_filter_increments = ${IAU_FILTER_INCREMENTS:-".false."}
 EOF
 fi