From 7d406643316163faf27d5b269a3313cdb08a50ce Mon Sep 17 00:00:00 2001
From: Cory Martin <cory.r.martin@noaa.gov>
Date: Tue, 26 Nov 2024 14:37:02 -0500
Subject: [PATCH] more changes for switching aerosol DA to JCB (#48)

---
 algorithm/aero/aero_gen_bmatrix_diagb.yaml.j2 | 21 ++++++++++++++++++-
 algorithm/aero/aero_obs_staging.yaml.j2       |  8 +++++++
 2 files changed, 28 insertions(+), 1 deletion(-)
 create mode 100644 algorithm/aero/aero_obs_staging.yaml.j2

diff --git a/algorithm/aero/aero_gen_bmatrix_diagb.yaml.j2 b/algorithm/aero/aero_gen_bmatrix_diagb.yaml.j2
index d1f3eda..d90756e 100644
--- a/algorithm/aero/aero_gen_bmatrix_diagb.yaml.j2
+++ b/algorithm/aero/aero_gen_bmatrix_diagb.yaml.j2
@@ -73,7 +73,26 @@ variables:
   - mass_fraction_of_sea_salt003_in_air
   - mass_fraction_of_sea_salt004_in_air
 
-rescale: {{ aero_diagb_rescale_factor }}    # rescales the filtered std. dev. by "rescale"
+global rescale:
+  geometry:
+    fms initialization:
+        namelist filename: "{{aero_fv3jedi_files_path}}/fmsmpp.nml"
+        field table filename: "{{aero_fv3jedi_files_path}}/field_table"
+    akbk: "{{aero_fv3jedi_files_path}}/akbk.nc4"
+    layout:
+    - {{ aero_layout_x }}
+    - {{ aero_layout_y }}
+    npx: {{ aero_npx_clim_b }}
+    npy: {{ aero_npy_clim_b }}
+    npz: {{ aero_npz_clim_b }}
+    field metadata override: "{{aero_fv3jedi_files_path}}/fv3jedi_fieldmetadata_restart.yaml"
+  rescale stddev:
+    filetype: fms restart
+    skip coupler file: true
+    datapath: {{ aero_rescale_b_path }}
+    filename_trcr: rescale.fv_tracer.res.nc
+    filename_cplr: rescale.coupler.res
+
 number of halo points: {{ aero_diagb_n_halo }}
 number of neighbors: {{ aero_diagb_n_neighbors }}
 simple smoothing:
diff --git a/algorithm/aero/aero_obs_staging.yaml.j2 b/algorithm/aero/aero_obs_staging.yaml.j2
new file mode 100644
index 0000000..0e5c992
--- /dev/null
+++ b/algorithm/aero/aero_obs_staging.yaml.j2
@@ -0,0 +1,8 @@
+mkdir:
+    - '{{aero_obsdatain_path}}'
+copy:
+    {% for observation_from_jcb in observations %}
+    {% if use_observer(observation_from_jcb) %}
+    - ['{{aero_obsdataroot_path}}/{{aero_obsdatain_prefix}}{{observation_from_jcb}}{{aero_obsdatain_suffix}}', '{{aero_obsdatain_path}}']
+    {% endif %}
+    {% endfor %}