From d39bf61570394730e17cd6508307ff7a624cd3cd Mon Sep 17 00:00:00 2001
From: DavidNew-NOAA <david.new@noaa.gov>
Date: Fri, 27 Sep 2024 17:58:09 +0000
Subject: [PATCH 01/18] Update jcb-gdas hash

---
 parm/jcb-gdas | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/parm/jcb-gdas b/parm/jcb-gdas
index 272d6d73c..614730134 160000
--- a/parm/jcb-gdas
+++ b/parm/jcb-gdas
@@ -1 +1 @@
-Subproject commit 272d6d73c0ceea5332fee005f59b3270527d10c7
+Subproject commit 6147301341339a0520d73cc191ba37b767fecc82

From 1fde5628322c984f28bb962b17943b4130b7d2ad Mon Sep 17 00:00:00 2001
From: DavidNew-NOAA <david.new@noaa.gov>
Date: Mon, 7 Oct 2024 17:55:48 +0000
Subject: [PATCH 02/18] Update

---
 parm/atm/jcb-base.yaml.j2 | 4 ++++
 parm/jcb-gdas             | 2 +-
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/parm/atm/jcb-base.yaml.j2 b/parm/atm/jcb-base.yaml.j2
index 6387fffbb..10c461e55 100644
--- a/parm/atm/jcb-base.yaml.j2
+++ b/parm/atm/jcb-base.yaml.j2
@@ -71,6 +71,8 @@ observations: all_observations
 crtm_coefficient_path: "{{ DATA }}/crtm/"
 
 # Naming conventions for observational files
+atmosphere_obsdataroot_path: "{{COM_OBS}}"
+
 atmosphere_obsdatain_path: "{{atm_obsdatain_path}}"
 atmosphere_obsdatain_prefix: "{{OPREFIX}}"
 atmosphere_obsdatain_suffix: ".tm00.nc"
@@ -80,6 +82,8 @@ atmosphere_obsdataout_prefix: diag_
 atmosphere_obsdataout_suffix: "_{{ current_cycle | to_YMDH }}.nc"
 
 # Naming conventions for bias correction files
+atmosphere_obsbiasroot_path: "{{COM_ATMOS_ANALYSIS_PREV}}"
+
 atmosphere_obsbiasin_path: "{{DATA}}/obs/"
 atmosphere_obsbiasin_prefix: "{{GPREFIX}}"
 atmosphere_obsbiasin_suffix: ".satbias.nc"
diff --git a/parm/jcb-gdas b/parm/jcb-gdas
index 614730134..b72f7bd1f 160000
--- a/parm/jcb-gdas
+++ b/parm/jcb-gdas
@@ -1 +1 @@
-Subproject commit 6147301341339a0520d73cc191ba37b767fecc82
+Subproject commit b72f7bd1f719cbb471ef2b94db8c930b21d15ad2

From 3bf7b50f324d4073cb357d0088bd11d324038593 Mon Sep 17 00:00:00 2001
From: DavidNew-NOAA <david.new@noaa.gov>
Date: Tue, 8 Oct 2024 01:12:07 +0000
Subject: [PATCH 03/18] Update JCB gdas hash

---
 parm/jcb-gdas | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/parm/jcb-gdas b/parm/jcb-gdas
index b72f7bd1f..803c0c758 160000
--- a/parm/jcb-gdas
+++ b/parm/jcb-gdas
@@ -1 +1 @@
-Subproject commit b72f7bd1f719cbb471ef2b94db8c930b21d15ad2
+Subproject commit 803c0c7580faf998ff1378c1a2d343aa8bbe508a

From 8a501f7905497f5b65649fd05c825f5869b2a6c8 Mon Sep 17 00:00:00 2001
From: DavidNew-NOAA <david.new@noaa.gov>
Date: Tue, 8 Oct 2024 16:36:14 +0000
Subject: [PATCH 04/18] Update jjob tests for new feature

---
 test/atm/global-workflow/config.yaml | 9 ++-------
 1 file changed, 2 insertions(+), 7 deletions(-)

diff --git a/test/atm/global-workflow/config.yaml b/test/atm/global-workflow/config.yaml
index c06019628..d8bf2e4c2 100644
--- a/test/atm/global-workflow/config.yaml
+++ b/test/atm/global-workflow/config.yaml
@@ -10,7 +10,7 @@ base:
   PTMP: "@bindir@/test/atm/global-workflow/testrun"
 
 atmanl:
-  JCB_ALGO_YAML: "@srcdir@/test/atm/global-workflow/jcb-prototype_3dvar.yaml.j2"
+  JCB_ALGO_YAML_VAR: "@srcdir@/test/atm/global-workflow/jcb-prototype_3dvar.yaml.j2"
   STATICB_TYPE: "identity"
   ATMRES_ANL: "C48"
   LAYOUT_X_ATMANL: 1
@@ -19,11 +19,6 @@ atmanl:
 atmensanl:
   JCB_ALGO_YAML_LETKF: "@srcdir@/test/atm/global-workflow/jcb-prototype_lgetkf.yaml.j2"
   JCB_ALGO_YAML_OBS: "@srcdir@/test/atm/global-workflow/jcb-prototype_lgetkf_observer.yaml.j2"
+  JCB_ALGO_YAML_SOL: "@srcdir@/test/atm/global-workflow/jcb-prototype_lgetkf_solver.yaml.j2"
   LAYOUT_X_ATMENSANL: 1
   LAYOUT_Y_ATMENSANL: 1
-
-atmensanlobs:
-  JCB_ALGO_YAML: "@srcdir@/test/atm/global-workflow/jcb-prototype_lgetkf_observer.yaml.j2"
-
-atmensanlsol:
-  JCB_ALGO_YAML: "@srcdir@/test/atm/global-workflow/jcb-prototype_lgetkf_solver.yaml.j2"

From 29696c82ab994e02dcfbeefc4b30953de352605b Mon Sep 17 00:00:00 2001
From: DavidNew-NOAA <david.new@noaa.gov>
Date: Wed, 9 Oct 2024 13:39:09 +0000
Subject: [PATCH 05/18] Change the way obs biases are staged

---
 parm/atm/jcb-base.yaml.j2 | 10 ++++++++++
 parm/jcb-gdas             |  2 +-
 2 files changed, 11 insertions(+), 1 deletion(-)

diff --git a/parm/atm/jcb-base.yaml.j2 b/parm/atm/jcb-base.yaml.j2
index 10c461e55..d7e1e5907 100644
--- a/parm/atm/jcb-base.yaml.j2
+++ b/parm/atm/jcb-base.yaml.j2
@@ -98,6 +98,16 @@ atmosphere_obsbiasout_suffix: ".satbias.nc"
 atmosphere_obsbiascovout_prefix: "{{APREFIX}}"
 atmosphere_obsbiascovout_suffix: ".satbias_cov.nc"
 
+bias_files:
+  atms_n20: rad_varbc_params.tar
+  atms_npp: rad_varbc_params.tar
+  mtiasi_metop-a: rad_varbc_params.tar
+  mtiasi_metop-b: rad_varbc_params.tar
+  amsua_n19: rad_varbc_params.tar
+  ssmis_f17: rad_varbc_params.tar
+  ssmis_f18: rad_varbc_params.tar
+  cris-fsr_n20: rad_varbc_params.tar
+  cris-fsr_npp: rad_varbc_params.tar
 
 # Local Ensemble DA (LETKF)
 # -------------------------
diff --git a/parm/jcb-gdas b/parm/jcb-gdas
index 803c0c758..6b0276175 160000
--- a/parm/jcb-gdas
+++ b/parm/jcb-gdas
@@ -1 +1 @@
-Subproject commit 803c0c7580faf998ff1378c1a2d343aa8bbe508a
+Subproject commit 6b02761758d607105579a9627f54c86aab01164a

From 140dc0e6a6550321b6cf1db6630f3d6ca067dc12 Mon Sep 17 00:00:00 2001
From: DavidNew-NOAA <david.new@noaa.gov>
Date: Wed, 9 Oct 2024 23:56:06 +0000
Subject: [PATCH 06/18] update jcb-gdas hash

---
 parm/jcb-gdas | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/parm/jcb-gdas b/parm/jcb-gdas
index 6b0276175..7717c0e74 160000
--- a/parm/jcb-gdas
+++ b/parm/jcb-gdas
@@ -1 +1 @@
-Subproject commit 6b02761758d607105579a9627f54c86aab01164a
+Subproject commit 7717c0e7401e344a6bce37a4f8ecc11399256936

From 6e85be032c18419fa245d7d0743264c70bd0592c Mon Sep 17 00:00:00 2001
From: DavidNew-NOAA <david.new@noaa.gov>
Date: Sun, 13 Oct 2024 20:24:26 +0000
Subject: [PATCH 07/18] Update JCB hash

---
 parm/jcb-gdas | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/parm/jcb-gdas b/parm/jcb-gdas
index 2b46aa19b..90e2c488b 160000
--- a/parm/jcb-gdas
+++ b/parm/jcb-gdas
@@ -1 +1 @@
-Subproject commit 2b46aa19b22df22f33ef0be5030fb719a8fa6298
+Subproject commit 90e2c488bc98aac00c0530bb47f1b5ff5be09bdf

From c9fd1837189f6d5efbc1b69e3429db0ea03769e1 Mon Sep 17 00:00:00 2001
From: DavidNew-NOAA <david.new@noaa.gov>
Date: Tue, 15 Oct 2024 00:30:21 +0000
Subject: [PATCH 08/18] Update marine JCB stuff

---
 parm/jcb-gdas                  | 2 +-
 parm/soca/marine-jcb-base.yaml | 8 ++++++--
 2 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/parm/jcb-gdas b/parm/jcb-gdas
index 90e2c488b..bed994ae7 160000
--- a/parm/jcb-gdas
+++ b/parm/jcb-gdas
@@ -1 +1 @@
-Subproject commit 90e2c488bc98aac00c0530bb47f1b5ff5be09bdf
+Subproject commit bed994ae7af44be7ce94c157dd2bb2735d64a8c0
diff --git a/parm/soca/marine-jcb-base.yaml b/parm/soca/marine-jcb-base.yaml
index cb5230f1c..95382e7f4 100644
--- a/parm/soca/marine-jcb-base.yaml
+++ b/parm/soca/marine-jcb-base.yaml
@@ -31,6 +31,10 @@ analysis_variables: [cicen, hicen, hsnon, socn, tocn, uocn, vocn, ssh]
 # ------------
 marine_window_begin: '{{MARINE_WINDOW_BEGIN}}'
 marine_window_middle: '{{MARINE_WINDOW_MIDDLE}}'
+marine_window_begin_iso: '{{ MARINE_WINDOW_BEGIN | to_isotime }}'
+marine_window_middle_iso: '{{ MARINE_WINDOW_MIDDLE | to_isotime }}'
+marine_window_end_iso: '{{ MARINE_WINDOW_END | to_isotime }}'
+enspert_relpath: '{{ ENSPERT_RELPATH }}'
 
 # Geometry
 marine_soca_files_path: .
@@ -42,11 +46,11 @@ marine_background_time: '{{MARINE_WINDOW_BEGIN_ISO}}'
 
 # Pseudo model
 marine_forecast_timestep: PT3H
-marine_pseudo_model_states: !INC 'bkg_list.yaml'
+#marine_pseudo_model_states: !INC 'bkg_list.yaml'
 
 # Background error model
 background_error_file: '{{berror_model}}'
-marine_number_ensemble_members: '{{nmem_ens}}'
+marine_number_ensemble_members: '{{NMEM_ENS}}'
 marine_stddev_time: '{{MARINE_WINDOW_MIDDLE}}'
 
 # Observations

From 52bc8d5ef7ad436e07da6baf5f15bbd8dac03104 Mon Sep 17 00:00:00 2001
From: DavidNew-NOAA <david.new@noaa.gov>
Date: Tue, 15 Oct 2024 02:26:58 +0000
Subject: [PATCH 09/18] Saving progress

---
 parm/soca/marine-jcb-base.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/parm/soca/marine-jcb-base.yaml b/parm/soca/marine-jcb-base.yaml
index 95382e7f4..c5b1d2825 100644
--- a/parm/soca/marine-jcb-base.yaml
+++ b/parm/soca/marine-jcb-base.yaml
@@ -17,7 +17,7 @@ final_increment_file: marine_final_increment
 
 # Assimilation standard things (not prepended with model choice)
 # ----------------------------
-window_begin: '{{MARINE_WINDOW_BEGIN}}'
+window_begin: '{{ MARINE_WINDOW_BEGIN | to_isotime }}'
 window_length: '{{MARINE_WINDOW_LENGTH}}'
 bound_to_include: begin
 minimizer: RPCG
@@ -38,7 +38,7 @@ enspert_relpath: '{{ ENSPERT_RELPATH }}'
 
 # Geometry
 marine_soca_files_path: .
-marine_vt_levels: '{{MOM6_LEVS}}'
+#marine_vt_levels: '{{MOM6_LEVS}}'
 
 # Initial conditions
 marine_background_path: ./INPUT/

From 9227d657b874be0768c1007bb22c9b3077bd3a0c Mon Sep 17 00:00:00 2001
From: DavidNew-NOAA <david.new@noaa.gov>
Date: Wed, 23 Oct 2024 15:54:04 +0000
Subject: [PATCH 10/18] Remove some unnecessary lines

---
 parm/soca/soca_fix_stage_500.yaml.j2 | 2 --
 parm/soca/soca_utils_stage.yaml.j2   | 1 -
 2 files changed, 3 deletions(-)

diff --git a/parm/soca/soca_fix_stage_500.yaml.j2 b/parm/soca/soca_fix_stage_500.yaml.j2
index 0b25073ba..9f030a81f 100644
--- a/parm/soca/soca_fix_stage_500.yaml.j2
+++ b/parm/soca/soca_fix_stage_500.yaml.j2
@@ -9,8 +9,6 @@ copy:
 - ["{{ SOCA_INPUT_FIX_DIR }}/field_table", "{{ DATA }}/field_table"]
 - ["{{ SOCA_INPUT_FIX_DIR }}/diag_table", "{{ DATA }}/diag_table"]
 - ["{{ SOCA_INPUT_FIX_DIR }}/MOM_input", "{{ DATA }}/MOM_input"]
-- ["{{ SOCA_INPUT_FIX_DIR }}/fields_metadata.yaml", "{{ DATA }}/fields_metadata.yaml"]
-- ["{{ SOCA_INPUT_FIX_DIR }}/obsop_name_map.yaml", "{{ DATA }}/obsop_name_map.yaml"]
 - ["{{ SOCA_INPUT_FIX_DIR }}/INPUT/grid_spec.nc", "{{ DATA }}/INPUT/grid_spec.nc"]
 - ["{{ SOCA_INPUT_FIX_DIR }}/INPUT/hycom1_25.nc", "{{ DATA }}/INPUT/hycom1_25.nc"]
 - ["{{ SOCA_INPUT_FIX_DIR }}/INPUT/layer_coord25.nc", "{{ DATA }}/INPUT/layer_coord25.nc"]
diff --git a/parm/soca/soca_utils_stage.yaml.j2 b/parm/soca/soca_utils_stage.yaml.j2
index 26570abe3..462cfccd0 100644
--- a/parm/soca/soca_utils_stage.yaml.j2
+++ b/parm/soca/soca_utils_stage.yaml.j2
@@ -4,4 +4,3 @@
 copy:
 - ["{{ HOMEgfs }}/parm/gdas/soca/fields_metadata.yaml", "{{ DATA }}/fields_metadata.yaml"]
 - ["{{ HOMEgfs }}/parm/gdas/soca/obsop_name_map.yaml", "{{ DATA }}/obsop_name_map.yaml"]
-- ["{{ HOMEgfs }}/parm/gdas/soca/gridgen/gridgen.yaml", "{{ DATA }}/gridgen.yaml"]

From a69df434d678419ca36b813f4f4c2836db5d28d5 Mon Sep 17 00:00:00 2001
From: DavidNew-NOAA <david.new@noaa.gov>
Date: Wed, 23 Oct 2024 15:54:31 +0000
Subject: [PATCH 11/18] Update JCB-GDAS hash

---
 parm/jcb-gdas | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/parm/jcb-gdas b/parm/jcb-gdas
index bed994ae7..f9b33faa6 160000
--- a/parm/jcb-gdas
+++ b/parm/jcb-gdas
@@ -1 +1 @@
-Subproject commit bed994ae7af44be7ce94c157dd2bb2735d64a8c0
+Subproject commit f9b33faa6c515e497949b0386ac669f93e062585

From b8ce7e16662eef62eec57244322aeac3d7e74d9a Mon Sep 17 00:00:00 2001
From: DavidNew-NOAA <david.new@noaa.gov>
Date: Wed, 23 Oct 2024 17:19:12 +0000
Subject: [PATCH 12/18] Uncomment a line

---
 parm/soca/marine-jcb-base.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/parm/soca/marine-jcb-base.yaml b/parm/soca/marine-jcb-base.yaml
index c5b1d2825..af09c952f 100644
--- a/parm/soca/marine-jcb-base.yaml
+++ b/parm/soca/marine-jcb-base.yaml
@@ -38,7 +38,7 @@ enspert_relpath: '{{ ENSPERT_RELPATH }}'
 
 # Geometry
 marine_soca_files_path: .
-#marine_vt_levels: '{{MOM6_LEVS}}'
+marine_vt_levels: '{{MOM6_LEVS}}'
 
 # Initial conditions
 marine_background_path: ./INPUT/

From a00b9191ce5253e984539024ab21ab3c44ece7f4 Mon Sep 17 00:00:00 2001
From: DavidNew-NOAA <david.new@noaa.gov>
Date: Wed, 23 Oct 2024 17:23:39 +0000
Subject: [PATCH 13/18] Update JCB GDAS hash

---
 parm/jcb-gdas | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/parm/jcb-gdas b/parm/jcb-gdas
index f9b33faa6..1061e52f9 160000
--- a/parm/jcb-gdas
+++ b/parm/jcb-gdas
@@ -1 +1 @@
-Subproject commit f9b33faa6c515e497949b0386ac669f93e062585
+Subproject commit 1061e52f9040c43801b96ce74493efd39f349736

From 1660f1ae50da47a1f6bc0c31c625bd3d185d93ca Mon Sep 17 00:00:00 2001
From: DavidNew-NOAA <david.new@noaa.gov>
Date: Thu, 24 Oct 2024 15:49:27 +0000
Subject: [PATCH 14/18] Update

---
 parm/soca/marine-jcb-base.yaml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/parm/soca/marine-jcb-base.yaml b/parm/soca/marine-jcb-base.yaml
index af09c952f..d07edcd8c 100644
--- a/parm/soca/marine-jcb-base.yaml
+++ b/parm/soca/marine-jcb-base.yaml
@@ -46,7 +46,6 @@ marine_background_time: '{{MARINE_WINDOW_BEGIN_ISO}}'
 
 # Pseudo model
 marine_forecast_timestep: PT3H
-#marine_pseudo_model_states: !INC 'bkg_list.yaml'
 
 # Background error model
 background_error_file: '{{berror_model}}'

From 12643982fade77a47e573da41a90198457e356be Mon Sep 17 00:00:00 2001
From: DavidNew-NOAA <david.new@noaa.gov>
Date: Thu, 24 Oct 2024 19:24:38 +0000
Subject: [PATCH 15/18] Remove YAMLs that are now in jcb-gdas

---
 parm/soca/berror/soca_diagb.yaml.j2           | 37 -------
 parm/soca/berror/soca_ensb.yaml.j2            | 98 -------------------
 parm/soca/berror/soca_ensweights.yaml.j2      | 37 -------
 .../soca_parameters_diffusion_hz.yaml.j2      | 37 -------
 .../soca_parameters_diffusion_vt.yaml.j2      | 33 -------
 parm/soca/berror/soca_setcorscales.yaml       | 23 -----
 parm/soca/berror/soca_vtscales.yaml.j2        | 13 ---
 7 files changed, 278 deletions(-)
 delete mode 100644 parm/soca/berror/soca_diagb.yaml.j2
 delete mode 100644 parm/soca/berror/soca_ensb.yaml.j2
 delete mode 100644 parm/soca/berror/soca_ensweights.yaml.j2
 delete mode 100644 parm/soca/berror/soca_parameters_diffusion_hz.yaml.j2
 delete mode 100644 parm/soca/berror/soca_parameters_diffusion_vt.yaml.j2
 delete mode 100644 parm/soca/berror/soca_setcorscales.yaml
 delete mode 100644 parm/soca/berror/soca_vtscales.yaml.j2

diff --git a/parm/soca/berror/soca_diagb.yaml.j2 b/parm/soca/berror/soca_diagb.yaml.j2
deleted file mode 100644
index c0597d358..000000000
--- a/parm/soca/berror/soca_diagb.yaml.j2
+++ /dev/null
@@ -1,37 +0,0 @@
-geometry:
-  mom6_input_nml: mom_input.nml
-  fields metadata: ./fields_metadata.yaml
-
-date: '{{ MARINE_WINDOW_END  | to_isotime }}'
-
-background:
-  date: '{{ MARINE_WINDOW_END  | to_isotime }}'
-  basename: ./bkg/
-  ocn_filename: 'ocean.bkg.f009.nc'
-  ice_filename: 'ice.bkg.f009.nc'
-  read_from_file: 1
-
-background error:
-  datadir: ./staticb/
-  date: '{{ MARINE_WINDOW_MIDDLE | to_isotime }}'
-  exp: bkgerr_stddev
-  type: incr
-
-variables:
-  name: [tocn, socn, uocn, vocn, hocn, ssh, cicen, hicen, hsnon, mom6_mld]
-
-rescale: 2.0    # rescales the filtered std. dev. by "rescale"
-min sst: 0.0    # Added to sst bkg. err.
-max ssh: 0.0    # Limits the amplitude of the unbalanced bkg err
-min depth: 500.0 # zero out the bkg. error. at less than min depth
-number of halo points: 4
-number of neighbors: 16
-
-simple smoothing:
-  horizontal iterations: 10
-  vertical iterations: 1
-
-# TODO(G): Too slow for the below scale
-#diffusion:
-#  horizontal: 500.0e3
-#  vertical: 3.0
diff --git a/parm/soca/berror/soca_ensb.yaml.j2 b/parm/soca/berror/soca_ensb.yaml.j2
deleted file mode 100644
index 4033f41ba..000000000
--- a/parm/soca/berror/soca_ensb.yaml.j2
+++ /dev/null
@@ -1,98 +0,0 @@
-# Configuration for the recentering and re-balancing of the ensemble members
-geometry:
-  mom6_input_nml: mom_input.nml
-  fields metadata: ./fields_metadata.yaml
-
-date: '{{ MARINE_WINDOW_BEGIN | to_isotime }}'
-
-layers variable: [hocn]
-
-increment variables: [tocn, socn, uocn, vocn, ssh, hocn, cicen, hicen, hsnon]
-
-set increment variables to zero: [ssh]
-
-vertical geometry:
-  date: '{{ MARINE_WINDOW_BEGIN | to_isotime }}'
-  basename: ./INPUT/
-  ocn_filename: MOM.res.nc
-  read_from_file: 3
-
-add recentering increment: false
-
-soca increments:  # Could also be states, but they are read as increments
-  number of increments: {{ NMEM_ENS }}
-  pattern: '%mem%'
-  template:
-    date: '{{ MARINE_WINDOW_BEGIN | to_isotime }}'
-    basename: '{{ ENSPERT_RELPATH }}/ens/'
-    ocn_filename: 'ocean.%mem%.nc'
-    ice_filename: 'ice.%mem%.nc'
-    read_from_file: 3
-
-steric height:
-  linear variable changes:
-  - linear variable change name: BalanceSOCA  # Only the steric balance is applied
-
-ensemble mean output:
-  datadir: ./staticb/
-  date: '{{ MARINE_WINDOW_BEGIN | to_isotime }}'
-  exp: ens_mean
-  type: incr
-
-ssh output:
-  unbalanced:
-    datadir: ./staticb/
-    date: '{{ MARINE_WINDOW_BEGIN | to_isotime }}'
-    exp: ssh_unbal_stddev
-    type: incr
-
-  steric:
-    datadir: ./staticb/
-    date: '{{ MARINE_WINDOW_BEGIN | to_isotime }}'
-    exp: ssh_steric_stddev
-    type: incr
-
-  total:
-    datadir: ./staticb/
-    date: '{{ MARINE_WINDOW_BEGIN | to_isotime }}'
-    exp: ssh_total_stddev
-    type: incr
-
-  explained variance:
-    datadir: ./staticb/
-    date: '{{ MARINE_WINDOW_BEGIN | to_isotime }}'
-    exp: steric_explained_variance
-    type: incr
-
-  recentering error:
-    datadir: ./staticb/
-    date: '{{ MARINE_WINDOW_BEGIN | to_isotime }}'
-    exp: ssh_recentering_error
-    type: incr
-
-background error output:
-  datadir: ./staticb/
-  date: '{{ MARINE_WINDOW_BEGIN | to_isotime }}'
-  exp: bkgerr_stddev
-  type: incr
-
-linear variable change:
-  linear variable changes:
-  - linear variable change name: BalanceSOCA
-
-trajectory:
-  state variables: [tocn, socn, uocn, vocn, ssh, hocn, layer_depth, mld, cicen, hicen, hsnon]
-  date: '{{ MARINE_WINDOW_BEGIN | to_isotime }}'
-  basename: ./INPUT/
-  ocn_filename: MOM.res.nc
-  ice_filename: cice.res.nc
-  read_from_file: 1
-
-output increment:
-  # TODO: Revert this when fms can take more than 128 charactres file names
-  datadir: '{{ ENSPERT_RELPATH }}/enspert/'
-  date: '{{ MARINE_WINDOW_BEGIN | to_isotime }}'
-  exp: trash
-  type: incr
-  output file: 'ocn.pert.steric.%mem%.nc'
-  pattern: '%mem%'
diff --git a/parm/soca/berror/soca_ensweights.yaml.j2 b/parm/soca/berror/soca_ensweights.yaml.j2
deleted file mode 100644
index f677d2a8d..000000000
--- a/parm/soca/berror/soca_ensweights.yaml.j2
+++ /dev/null
@@ -1,37 +0,0 @@
-geometry:
-  mom6_input_nml: mom_input.nml
-  fields metadata: ./fields_metadata.yaml
-
-date: '{{ MARINE_WINDOW_MIDDLE | to_isotime }}'
-
-variables:
-  ice: [cicen, hicen, hsnon]
-  ocean: [tocn, socn, uocn, vocn, ssh]
-
-background:
-  date: '{{ MARINE_WINDOW_BEGIN | to_isotime }}'
-  basename: ./INPUT/
-  ocn_filename: MOM.res.nc
-  ice_filename: cice.res.nc
-  read_from_file: 1
-
-weights:
-  # Need to provide weights^2 when reading from file
-  ice: 0.0025   #  5% of original variance
-  ocean: 0.0625   # 25%      "       "
-  # Apply localized weights to the ocean ens. B
-  ocean local weights:
-  - lon: -172.0
-    lat: 11.0
-    amplitude: -1.0
-    length scale: 700.0
-  - lon: -160.0
-    lat: 12.0
-    amplitude: -1.0
-    length scale: 700.0
-
-output:
-  datadir: ./
-  date: '{{ MARINE_WINDOW_MIDDLE | to_isotime }}'
-  exp: ens_weights
-  type: incr
diff --git a/parm/soca/berror/soca_parameters_diffusion_hz.yaml.j2 b/parm/soca/berror/soca_parameters_diffusion_hz.yaml.j2
deleted file mode 100644
index 7d3a78cfb..000000000
--- a/parm/soca/berror/soca_parameters_diffusion_hz.yaml.j2
+++ /dev/null
@@ -1,37 +0,0 @@
-geometry: &geom
-  mom6_input_nml: mom_input.nml
-  fields metadata: ./fields_metadata.yaml
-
-background:
-  read_from_file: 1
-  basename: ./INPUT/
-  ocn_filename: MOM.res.nc
-  ice_filename: cice.res.nc
-  date: '{{ MARINE_WINDOW_END  | to_isotime }}'
-  state variables: [ssh]
-
-background error:
-  covariance model: SABER
-  saber central block:
-    saber block name: diffusion
-    geometry: *geom
-    calibration:
-      normalization:
-        method: randomization
-        iterations: 10000
-
-      groups:
-      - horizontal:
-          model file:
-            date: '{{ MARINE_WINDOW_END  | to_isotime }}'
-            basename: ./
-            ocn_filename: ocn.cor_rh.incr.0001-01-01T00:00:00Z.nc
-          model variable: ssh
-        write:
-          filepath: ./staticb/hz_ocean
-
-      - horizontal:
-          as gaussian: true
-          fixed value: 50000.0
-        write:
-          filepath: ./staticb/hz_ice
diff --git a/parm/soca/berror/soca_parameters_diffusion_vt.yaml.j2 b/parm/soca/berror/soca_parameters_diffusion_vt.yaml.j2
deleted file mode 100644
index 76ab67e94..000000000
--- a/parm/soca/berror/soca_parameters_diffusion_vt.yaml.j2
+++ /dev/null
@@ -1,33 +0,0 @@
-geometry: &geom
-  mom6_input_nml: mom_input.nml
-  fields metadata: ./fields_metadata.yaml
-
-background:
-  read_from_file: 1
-  basename: ./INPUT/
-  ocn_filename: MOM.res.nc
-  ice_filename: cice.res.nc
-  date: '{{ MARINE_WINDOW_MIDDLE | to_isotime }}'
-  state variables: [tocn]
-
-background error:
-  covariance model: SABER
-  saber central block:
-    saber block name: diffusion
-    geometry: *geom
-    calibration:
-      normalization:
-        # NOTE, not actually used here, since the normalization spec is only used for hz
-        method: randomization  #< other option is "brute force"
-        iterations: 1000       #< in the real world you'll want to use 1e4 or so
-
-      groups:
-      - vertical:
-          as gaussian: true
-          model file:
-            date: '{{ MARINE_WINDOW_MIDDLE | to_isotime }}'
-            basename: ./
-            ocn_filename: vt_scales.nc
-          model variable: tocn
-        write:
-          filepath: ./staticb/vt_ocean
diff --git a/parm/soca/berror/soca_setcorscales.yaml b/parm/soca/berror/soca_setcorscales.yaml
deleted file mode 100644
index 0a91777a1..000000000
--- a/parm/soca/berror/soca_setcorscales.yaml
+++ /dev/null
@@ -1,23 +0,0 @@
-resolution:
-  mom6_input_nml: mom_input.nml
-  fields metadata: ./fields_metadata.yaml
-
-date: 0001-01-01T00:00:00Z
-
-corr variables: [ssh]
-
-scales:
-  vert layers: 5 # in units of layer
-  ssh:
-    rossby mult: 1.00
-    min grid mult: 2.0
-
-rh output:
-  datadir: ./
-  exp: cor_rh
-  type: incr
-
-rv output:
-  datadir: ./
-  exp: cor_rv
-  type: incr
diff --git a/parm/soca/berror/soca_vtscales.yaml.j2 b/parm/soca/berror/soca_vtscales.yaml.j2
deleted file mode 100644
index 8f68b1517..000000000
--- a/parm/soca/berror/soca_vtscales.yaml.j2
+++ /dev/null
@@ -1,13 +0,0 @@
-gridspec_filename: soca_gridspec.nc
-restart_filename: ./INPUT/MOM.res.nc
-mld_filename: './staticb/ocn.bkgerr_stddev.incr.{{ MARINE_WINDOW_END | to_isotime }}.nc'
-output_filename: ./vt_scales.nc
-output_variable_vt: Temp
-output_variable_hz: ave_ssh
-
-VT_MIN: 5
-VT_MAX: 15
-
-HZ_ROSSBY_MULT: 1.0
-HZ_MAX: 200e3
-HZ_MIN_GRID_MULT: 2.0

From 3d8892c503f0b57abdbf1e6aec750cfd45e90722 Mon Sep 17 00:00:00 2001
From: DavidNew-NOAA <david.new@noaa.gov>
Date: Thu, 31 Oct 2024 17:29:41 +0000
Subject: [PATCH 16/18] Update jcb-gdas hash

---
 parm/jcb-gdas | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/parm/jcb-gdas b/parm/jcb-gdas
index 1061e52f9..7fb998b81 160000
--- a/parm/jcb-gdas
+++ b/parm/jcb-gdas
@@ -1 +1 @@
-Subproject commit 1061e52f9040c43801b96ce74493efd39f349736
+Subproject commit 7fb998b8123423881574c55cd7674401c1c2e0f0

From 54e21096bbbea4d2a051149bf9c4073627c79622 Mon Sep 17 00:00:00 2001
From: DavidNew-NOAA <david.new@noaa.gov>
Date: Fri, 1 Nov 2024 14:46:58 +0000
Subject: [PATCH 17/18] Update jcb-gdas branch

---
 parm/jcb-gdas                  | 2 +-
 parm/soca/gridgen/gridgen.yaml | 5 -----
 2 files changed, 1 insertion(+), 6 deletions(-)
 delete mode 100644 parm/soca/gridgen/gridgen.yaml

diff --git a/parm/jcb-gdas b/parm/jcb-gdas
index 7fb998b81..b8e995a4c 160000
--- a/parm/jcb-gdas
+++ b/parm/jcb-gdas
@@ -1 +1 @@
-Subproject commit 7fb998b8123423881574c55cd7674401c1c2e0f0
+Subproject commit b8e995a4cbf01fa4a662c3da3e7d818f8457ec4e
diff --git a/parm/soca/gridgen/gridgen.yaml b/parm/soca/gridgen/gridgen.yaml
deleted file mode 100644
index 34fbdeca6..000000000
--- a/parm/soca/gridgen/gridgen.yaml
+++ /dev/null
@@ -1,5 +0,0 @@
-geometry:
-  geom_grid_file: soca_gridspec.nc
-  mom6_input_nml: mom_input.nml
-  fields metadata: fields_metadata.yaml
-  rossby file: rossrad.nc

From a658d59d1a7df426507ba66081979f1bb0ba7441 Mon Sep 17 00:00:00 2001
From: DavidNew-NOAA <david.new@noaa.gov>
Date: Thu, 31 Oct 2024 17:29:41 +0000
Subject: [PATCH 18/18] Update jcb-gdas hash

---
 parm/jcb-gdas | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/parm/jcb-gdas b/parm/jcb-gdas
index 7717c0e74..7fb998b81 160000
--- a/parm/jcb-gdas
+++ b/parm/jcb-gdas
@@ -1 +1 @@
-Subproject commit 7717c0e7401e344a6bce37a4f8ecc11399256936
+Subproject commit 7fb998b8123423881574c55cd7674401c1c2e0f0