From a41a0dba9a5b212ec2b36741839fb7d0cfffcc64 Mon Sep 17 00:00:00 2001
From: RussTreadon-NOAA <Russ.Treadon@noaa.gov>
Date: Thu, 8 Feb 2024 18:14:14 +0000
Subject: [PATCH] updates to populate EXPDIR and ROTDIR for JEDI hybatmDA ci
 (#2294)

---
 ci/cases/pr/C48C48_ufs_hybatmDA.yaml | 6 +++---
 parm/config/gfs/config.esfc          | 5 +++++
 parm/config/gfs/config.nsst          | 5 +++++
 parm/config/gfs/config.sfcanl        | 5 +++++
 workflow/setup_expt.py               | 2 +-
 5 files changed, 19 insertions(+), 4 deletions(-)

diff --git a/ci/cases/pr/C48C48_ufs_hybatmDA.yaml b/ci/cases/pr/C48C48_ufs_hybatmDA.yaml
index 1dd2a00c01..b0f7a2908c 100644
--- a/ci/cases/pr/C48C48_ufs_hybatmDA.yaml
+++ b/ci/cases/pr/C48C48_ufs_hybatmDA.yaml
@@ -9,13 +9,13 @@ arguments:
   resensatmos: 48
   comroot: {{ 'RUNTESTS' | getenv }}/COMROOT
   expdir: {{ 'RUNTESTS' | getenv }}/EXPDIR
-  icsdir: {{ 'ICSDIR_ROOT' | getenv }}/C96C48
+  icsdir: {{ 'ICSDIR_ROOT' | getenv }}/C48C48
   idate: 2021032312
   edate: 2021032400
   nens: 2
   gfs_cyc: 1
-  start: cold
-  yaml: {{ HOMEgfs }}/ci/cases/yamls/ufs_hybatmDA_defaults_ci.yaml
+  start: warm
+  yaml: {{ HOMEgfs }}/ci/cases/yamls/ufs_hybatmDA_defaults.ci.yaml
 
 skip_ci_on_hosts:
   - orion
diff --git a/parm/config/gfs/config.esfc b/parm/config/gfs/config.esfc
index 2bb3d48bb4..7a5bce4681 100644
--- a/parm/config/gfs/config.esfc
+++ b/parm/config/gfs/config.esfc
@@ -16,4 +16,9 @@ if [ $DOIAU_ENKF = "YES" ]; then
    export DOSFCANL_ENKF="NO"
 fi
 
+# Turn off NST in JEDIATMENS
+if [ $DO_JEDIATMENS = "YES" ]; then
+   export DONST="NO"
+fi
+
 echo "END: config.esfc"
diff --git a/parm/config/gfs/config.nsst b/parm/config/gfs/config.nsst
index db4367b2c0..a85e87b47f 100644
--- a/parm/config/gfs/config.nsst
+++ b/parm/config/gfs/config.nsst
@@ -10,6 +10,11 @@ echo "BEGIN: config.nsst"
 # nstf_name(1) : NST_MODEL (NSST Model) : 0 = OFF, 1 = ON but uncoupled, 2 = ON and coupled
 export NST_MODEL=2
 
+# Set NST_MODEL for JEDIATMVAR or JEDIATMENS
+if [[ $DO_JEDIATMVAR = "YES" || $DO_JEDIATMENS = "YES" ]]; then
+   export NST_MODEL=1
+fi
+
 # nstf_name(2) : NST_SPINUP : 0 = OFF, 1 = ON,
 export NST_SPINUP=0
 cdate="${PDY}${cyc}"
diff --git a/parm/config/gfs/config.sfcanl b/parm/config/gfs/config.sfcanl
index 9592fb77c9..aa08f5a692 100644
--- a/parm/config/gfs/config.sfcanl
+++ b/parm/config/gfs/config.sfcanl
@@ -8,4 +8,9 @@ echo "BEGIN: config.sfcanl"
 # Get task specific resources
 . $EXPDIR/config.resources sfcanl
 
+# Turn off NST in JEDIATMVAR
+if [ $DO_JEDIATMVAR = "YES" ]; then
+   export DONST="NO"
+fi
+
 echo "END: config.sfcanl"
diff --git a/workflow/setup_expt.py b/workflow/setup_expt.py
index 2bc41854d8..06af4d3d2b 100755
--- a/workflow/setup_expt.py
+++ b/workflow/setup_expt.py
@@ -219,7 +219,7 @@ def link_files_from_src_to_dst(src_dir, dst_dir):
     src_dir = os.path.join(inputs.icsdir, current_cycle_dir, src_atm_anl_dir)
     dst_dir = os.path.join(rotdir, current_cycle_dir, dst_atm_anl_dir)
     makedirs_if_missing(dst_dir)
-    for ftype in ['abias', 'abias_pc', 'abias_air', 'radstat']:
+    for ftype in ['abias', 'abias_pc', 'abias_air', 'radstat', 'atms_n20.satbias.nc4', 'atms_n20.satbias_cov.nc4', 'atms_n20.tlapse.txt' ]:
         fname = f'{inputs.cdump}.t{idatestr[8:]}z.{ftype}'
         src_file = os.path.join(src_dir, fname)
         if os.path.exists(src_file):