diff --git a/.github/workflows/run_jcb_basic_testing.yaml b/.github/workflows/run_jcb_basic_testing.yaml
new file mode 100644
index 000000000..d8d4b1295
--- /dev/null
+++ b/.github/workflows/run_jcb_basic_testing.yaml
@@ -0,0 +1,121 @@
+name: Run JCB client testing with client changes
+
+on:
+ push:
+ branches:
+ - develop
+ pull_request:
+ types:
+ - opened
+ - synchronize
+ - reopened
+
+jobs:
+
+ jcb_integration_tests:
+
+ runs-on: ubuntu-latest
+ name: JCB Client Integration Tests
+
+ env:
+ JCB_REPO: https://github.com/NOAA-EMC/jcb.git
+
+ steps:
+ - name: Set up Python
+ uses: actions/setup-python@v4
+ with:
+ python-version: '3.x'
+
+ - name: Add repo url to the environment
+ run: |
+ JCB_APP_REPO="${{ github.repository }}"
+ echo "JCB_APP_REPO=${JCB_APP_REPO}" >> $GITHUB_ENV
+
+ - name: Determine the name of the client branch
+ run: |
+ if [ "${{ github.event_name }}" == "pull_request" ]; then
+ JCB_APP_BRANCH=${{ github.head_ref }}
+ else
+ BRANCH_REF=${{ github.ref }}
+ JCB_APP_BRANCH=${BRANCH_REF#refs/heads/}
+ fi
+ echo "JCB_APP_BRANCH=$JCB_APP_BRANCH" >> $GITHUB_ENV
+
+ - name: Determine branch to use for main jcb repo
+ run: |
+ BRANCH_NAME=${{ env.JCB_APP_BRANCH }}
+ if git ls-remote --heads $JCB_REPO $BRANCH_NAME | grep -q "refs/heads/$BRANCH_NAME"; then
+ echo "Branch $BRANCH_NAME exists in jcb repo."
+ echo "JCB_BRANCH=$BRANCH_NAME" >> $GITHUB_ENV
+ else
+ echo "Branch $BRANCH_NAME does not exist in jcb repo. Using develop branch."
+ echo "JCB_BRANCH=develop" >> $GITHUB_ENV
+ fi
+
+ - name: Check for the branch name in the jcb-algorithms repo (if not develop)
+ run: |
+ BRANCH_NAME=${{ env.JCB_APP_BRANCH }}
+
+ # If branch name is develop then we don't need to check the jcb-algorithms repo.
+ if [ "$BRANCH_NAME" == "develop" ]; then
+ echo "JCB_ALGO_BRANCH=develop" >> $GITHUB_ENV
+ exit 0
+ fi
+
+ # If the branch is not develop then check the jcb-algorithms repo.
+ if git ls-remote --heads https://github.com/NOAA-EMC/jcb-algorithms.git $BRANCH_NAME | grep -q "refs/heads/$BRANCH_NAME"; then
+ echo "Branch $BRANCH_NAME exists in jcb-algorithms repo."
+ echo "JCB_ALGO_BRANCH=$BRANCH_NAME" >> $GITHUB_ENV
+
+ # If the branch exists in jcb-algorithms repo but JCB_BRANCH is develop then we need to
+ # throw an error. This is not a safe situation. The developer should create a branch in
+ # the main jcb repo with the same name as the branch in the jcb-application repo.
+ # If there were branches in other apps to account for the changes in the algorithm repo
+ # they could not be tested here since the scipt is not clever enough to check for
+ # the existence of the branch being tested here in all the clients. The safest thing to do
+ # is simply create a branch with the same name (even if empty) in the main jcb repo. This
+ # will ensure the branches of the other applications are checked out by the init script.
+
+ if [ "${{ env.JCB_BRANCH }}" == "develop" ]; then
+ echo "Branch $BRANCH_NAME exists in jcb-algorithms repo but not in the main jcb repo. "
+ echo "Please create a branch with the same name (even if empty with no PR) in the main "
+ echo "jcb repo. This ensures safely checking all the clients that depend on the "
+ echo "jcb and jcb-algorithms repos with the changes being proposed."
+ exit 1
+ fi
+ fi
+
+ - name: Clone jcb repository
+ run: |
+ mkdir -p empty_hooks
+ git config --global core.hooksPath empty_hooks
+ git clone --branch ${{ env.JCB_BRANCH }} --recursive $JCB_REPO jcb_repo
+
+ - name: Create custom jcb_clients.yaml for isolated testing
+ run: |
+ cd jcb_repo
+
+ # Create a custom jcb_clients.yaml that only includes the current repository
+ cat > jcb_clients.yaml << EOF
+ gdas:
+ git_url: noaa-emc/gdasapp
+ #git_ref: develop
+ git_ref: feature/jcb-gdas
+ app_subdir: parm/jcb-gdas
+ EOF
+
+ - name: Clone the clients
+ run: |
+ cd jcb_repo
+ pip install pyyaml
+ ./jcb_client_init.py
+
+ - name: Install dependencies
+ run: |
+ cd jcb_repo
+ pip install .[testing]
+
+ - name: Run the JCB client integration tests
+ run: |
+ cd jcb_repo/test/client_integration
+ pytest -v
diff --git a/.gitmodules b/.gitmodules
index 6ca2dbc18..4319b5d63 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -53,10 +53,6 @@
path = sorc/jcb
url = https://github.com/noaa-emc/jcb.git
branch = develop
-[submodule "parm/jcb-gdas"]
- path = parm/jcb-gdas
- url = https://github.com/noaa-emc/jcb-gdas
- branch = develop
[submodule "parm/jcb-algorithms"]
path = parm/jcb-algorithms
url = https://github.com/noaa-emc/jcb-algorithms
diff --git a/parm/jcb-gdas b/parm/jcb-gdas
deleted file mode 160000
index 5891b215d..000000000
--- a/parm/jcb-gdas
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit 5891b215d82ffae1cb27aa203c6161dcc523b541
diff --git a/parm/jcb-gdas/.gitignore b/parm/jcb-gdas/.gitignore
new file mode 100644
index 000000000..5509140f2
--- /dev/null
+++ b/parm/jcb-gdas/.gitignore
@@ -0,0 +1 @@
+*.DS_Store
diff --git a/parm/jcb-gdas/LICENSE b/parm/jcb-gdas/LICENSE
new file mode 100644
index 000000000..f288702d2
--- /dev/null
+++ b/parm/jcb-gdas/LICENSE
@@ -0,0 +1,674 @@
+ GNU GENERAL PUBLIC LICENSE
+ Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc.
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
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diff --git a/parm/jcb-gdas/algorithm/aero/aero_addincrement.yaml.j2 b/parm/jcb-gdas/algorithm/aero/aero_addincrement.yaml.j2
new file mode 100644
index 000000000..895995ee4
--- /dev/null
+++ b/parm/jcb-gdas/algorithm/aero/aero_addincrement.yaml.j2
@@ -0,0 +1,43 @@
+state geometry:
+ fms initialization:
+ namelist filename: ./fv3jedi/fmsmpp.nml
+ field table filename: ./fv3jedi/field_table
+ akbk: ./fv3jedi/akbk.nc4
+ layout:
+ - {{ aero_layout_x }}
+ - {{ aero_layout_y }}
+ npx: {{ aero_npx_ges }}
+ npy: {{ aero_npy_ges }}
+ npz: {{ aero_npz_ges }}
+ field metadata override: ./fv3jedi/fv3jedi_fieldmetadata_history.yaml
+increment geometry:
+ fms initialization:
+ namelist filename: ./fv3jedi/fmsmpp.nml
+ field table filename: ./fv3jedi/field_table
+ akbk: ./fv3jedi/akbk.nc4
+ layout:
+ - {{ aero_layout_x }}
+ - {{ aero_layout_y }}
+ npx: {{ aero_npx_ges }}
+ npy: {{ aero_npy_ges }}
+ npz: {{ aero_npz_ges }}
+ field metadata override: ./fv3jedi/fv3jedi_fieldmetadata_restart.yaml
+state:
+ datetime: '{{ aero_background_time_iso }}'
+ state variables: {{ analysis_variables }}
+ filetype: cube sphere history
+ provider: ufs
+ datapath: ./
+ filename: {{ aero_variational_history_prefix }}cubed_sphere_grid_atmf006.nc
+increment:
+ added variables: {{ analysis_variables }}
+ filetype: fms restart
+ datapath: ./
+ filename is datetime templated: true
+ filename_trcr: '%yyyy%mm%dd.%hh%MM%ss.fv_tracer.res.nc'
+ prefix: aeroinc
+output:
+ filetype: auxgrid
+ gridtype: gaussian
+ datapath: ./
+ filename: aeroanl.
diff --git a/parm/jcb-gdas/algorithm/aero/aero_convert_background.yaml.j2 b/parm/jcb-gdas/algorithm/aero/aero_convert_background.yaml.j2
new file mode 100644
index 000000000..7b4d38c0e
--- /dev/null
+++ b/parm/jcb-gdas/algorithm/aero/aero_convert_background.yaml.j2
@@ -0,0 +1,84 @@
+input 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_ges }}
+ npy: {{ aero_npy_ges }}
+ npz: {{ aero_npz_ges }}
+output 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_anl }}
+ npy: {{ aero_npy_anl }}
+ npz: {{ aero_npz_anl }}
+states:
+- input:
+ datetime: '{{ aero_background_error_time_iso }}'
+ filetype: fms restart
+ state variables:
+ - mass_fraction_of_sulfate_in_air
+ - mass_fraction_of_hydrophobic_black_carbon_in_air
+ - mass_fraction_of_hydrophilic_black_carbon_in_air
+ - mass_fraction_of_hydrophobic_organic_carbon_in_air
+ - mass_fraction_of_hydrophilic_organic_carbon_in_air
+ - mass_fraction_of_dust001_in_air
+ - mass_fraction_of_dust002_in_air
+ - mass_fraction_of_dust003_in_air
+ - mass_fraction_of_dust004_in_air
+ - mass_fraction_of_dust005_in_air
+ - mass_fraction_of_sea_salt001_in_air
+ - mass_fraction_of_sea_salt002_in_air
+ - mass_fraction_of_sea_salt003_in_air
+ - mass_fraction_of_sea_salt004_in_air
+ - mass_fraction_of_sea_salt005_in_air
+ field io names:
+ mass_fraction_of_dust001_in_air: dust1
+ mass_fraction_of_dust002_in_air: dust2
+ mass_fraction_of_dust003_in_air: dust3
+ mass_fraction_of_dust004_in_air: dust4
+ mass_fraction_of_dust005_in_air: dust5
+ mass_fraction_of_sea_salt001_in_air: seas1
+ mass_fraction_of_sea_salt002_in_air: seas2
+ mass_fraction_of_sea_salt003_in_air: seas3
+ mass_fraction_of_sea_salt004_in_air: seas4
+ mass_fraction_of_sea_salt005_in_air: seas5
+ mass_fraction_of_hydrophobic_black_carbon_in_air: bc1
+ mass_fraction_of_hydrophilic_black_carbon_in_air: bc2
+ mass_fraction_of_hydrophobic_organic_carbon_in_air: oc1
+ mass_fraction_of_hydrophilic_organic_carbon_in_air: oc2
+ mass_fraction_of_sulfate_in_air: so4
+ datapath: {{ aero_background_path }}
+ filename_core: '{{ aero_background_error_time_fv3 }}.fv_core.res.nc'
+ filename_trcr: '{{ aero_background_error_time_fv3 }}.fv_tracer.res.nc'
+ filename_cplr: '{{ aero_background_error_time_fv3 }}.coupler.res'
+ output:
+ filetype: fms restart
+ datapath: {{ aero_background_path }}
+ filename_core: 'anlres.fv_core.res.nc'
+ filename_trcr: 'anlres.fv_tracer.res.nc'
+ filename_cplr: 'anlres.coupler.res'
+ field io names:
+ mass_fraction_of_dust001_in_air: dust1
+ mass_fraction_of_dust002_in_air: dust2
+ mass_fraction_of_dust003_in_air: dust3
+ mass_fraction_of_dust004_in_air: dust4
+ mass_fraction_of_dust005_in_air: dust5
+ mass_fraction_of_sea_salt001_in_air: seas1
+ mass_fraction_of_sea_salt002_in_air: seas2
+ mass_fraction_of_sea_salt003_in_air: seas3
+ mass_fraction_of_sea_salt004_in_air: seas4
+ mass_fraction_of_sea_salt005_in_air: seas5
+ mass_fraction_of_hydrophobic_black_carbon_in_air: bc1
+ mass_fraction_of_hydrophilic_black_carbon_in_air: bc2
+ mass_fraction_of_hydrophobic_organic_carbon_in_air: oc1
+ mass_fraction_of_hydrophilic_organic_carbon_in_air: oc2
+ mass_fraction_of_sulfate_in_air: so4
diff --git a/parm/jcb-gdas/algorithm/aero/aero_gen_bmatrix_diagb.yaml.j2 b/parm/jcb-gdas/algorithm/aero/aero_gen_bmatrix_diagb.yaml.j2
new file mode 100644
index 000000000..62e88a91a
--- /dev/null
+++ b/parm/jcb-gdas/algorithm/aero/aero_gen_bmatrix_diagb.yaml.j2
@@ -0,0 +1,147 @@
+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_anl }}
+ npy: {{ aero_npy_anl }}
+ npz: {{ aero_npz_anl }}
+ time invariant fields:
+ state fields:
+ datetime: '{{ aero_background_error_time_iso }}'
+ filetype: fms restart
+ skip coupler file: true
+ state variables:
+ - slmsk
+ field io names:
+ slmsk: slmsk
+ datapath: {{ aero_background_path }}/
+ filename_orog: {{ aero_orog_prefix }}_oro_data.nc
+ filename_sfcd: {{ aero_background_error_time_fv3 }}.sfc_data.nc
+date: '{{ aero_background_error_time_iso }}'
+background:
+ datetime: '{{ aero_background_error_time_iso }}'
+ filetype: fms restart
+ state variables:
+ - mass_fraction_of_sulfate_in_air
+ - mass_fraction_of_hydrophobic_black_carbon_in_air
+ - mass_fraction_of_hydrophilic_black_carbon_in_air
+ - mass_fraction_of_hydrophobic_organic_carbon_in_air
+ - mass_fraction_of_hydrophilic_organic_carbon_in_air
+ - mass_fraction_of_dust001_in_air
+ - mass_fraction_of_dust002_in_air
+ - mass_fraction_of_dust003_in_air
+ - mass_fraction_of_dust004_in_air
+ - mass_fraction_of_dust005_in_air
+ - mass_fraction_of_sea_salt001_in_air
+ - mass_fraction_of_sea_salt002_in_air
+ - mass_fraction_of_sea_salt003_in_air
+ - mass_fraction_of_sea_salt004_in_air
+ - mass_fraction_of_sea_salt005_in_air
+ field io names:
+ mass_fraction_of_dust001_in_air: dust1
+ mass_fraction_of_dust002_in_air: dust2
+ mass_fraction_of_dust003_in_air: dust3
+ mass_fraction_of_dust004_in_air: dust4
+ mass_fraction_of_dust005_in_air: dust5
+ mass_fraction_of_sea_salt001_in_air: seas1
+ mass_fraction_of_sea_salt002_in_air: seas2
+ mass_fraction_of_sea_salt003_in_air: seas3
+ mass_fraction_of_sea_salt004_in_air: seas4
+ mass_fraction_of_sea_salt005_in_air: seas5
+ mass_fraction_of_hydrophobic_black_carbon_in_air: bc1
+ mass_fraction_of_hydrophilic_black_carbon_in_air: bc2
+ mass_fraction_of_hydrophobic_organic_carbon_in_air: oc1
+ mass_fraction_of_hydrophilic_organic_carbon_in_air: oc2
+ mass_fraction_of_sulfate_in_air: so4
+ datapath: {{ aero_background_path }}
+ filename_core: '{{ aero_background_error_time_fv3 }}.anlres.fv_core.res.nc'
+ filename_trcr: '{{ aero_background_error_time_fv3 }}.anlres.fv_tracer.res.nc'
+ filename_cplr: '{{ aero_background_error_time_fv3 }}.anlres.coupler.res'
+background error:
+ filetype: fms restart
+ datapath: {{ aero_standard_deviation_path }}
+ filename_trcr: stddev.fv_tracer.res.nc
+ filename_cplr: stddev.coupler.res
+ field io names:
+ mass_fraction_of_dust001_in_air: dust1
+ mass_fraction_of_dust002_in_air: dust2
+ mass_fraction_of_dust003_in_air: dust3
+ mass_fraction_of_dust004_in_air: dust4
+ mass_fraction_of_dust005_in_air: dust5
+ mass_fraction_of_sea_salt001_in_air: seas1
+ mass_fraction_of_sea_salt002_in_air: seas2
+ mass_fraction_of_sea_salt003_in_air: seas3
+ mass_fraction_of_sea_salt004_in_air: seas4
+ mass_fraction_of_sea_salt005_in_air: seas5
+ mass_fraction_of_hydrophobic_black_carbon_in_air: bc1
+ mass_fraction_of_hydrophilic_black_carbon_in_air: bc2
+ mass_fraction_of_hydrophobic_organic_carbon_in_air: oc1
+ mass_fraction_of_hydrophilic_organic_carbon_in_air: oc2
+ mass_fraction_of_sulfate_in_air: so4
+climate background error:
+ 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 }}
+ climate background error stddev:
+ filetype: fms restart
+ skip coupler file: true
+ datapath: {{ aero_climatological_b_path }}
+ filename_trcr: stddev.fv_tracer.res.nc
+ filename_cplr: stddev.coupler.res
+ field io names:
+ mass_fraction_of_dust001_in_air: dust1
+ mass_fraction_of_dust002_in_air: dust2
+ mass_fraction_of_dust003_in_air: dust3
+ mass_fraction_of_dust004_in_air: dust4
+ mass_fraction_of_dust005_in_air: dust5
+ mass_fraction_of_sea_salt001_in_air: seas1
+ mass_fraction_of_sea_salt002_in_air: seas2
+ mass_fraction_of_sea_salt003_in_air: seas3
+ mass_fraction_of_sea_salt004_in_air: seas4
+ mass_fraction_of_sea_salt005_in_air: seas5
+ mass_fraction_of_hydrophobic_black_carbon_in_air: bc1
+ mass_fraction_of_hydrophilic_black_carbon_in_air: bc2
+ mass_fraction_of_hydrophobic_organic_carbon_in_air: oc1
+ mass_fraction_of_hydrophilic_organic_carbon_in_air: oc2
+ mass_fraction_of_sulfate_in_air: so4
+ diagb weight: {{ aero_diagb_weight }}
+ staticb rescaling factor: {{ aero_diagb_static_rescale_factor }}
+
+variables:
+ name:
+ - mass_fraction_of_sulfate_in_air
+ - mass_fraction_of_hydrophobic_black_carbon_in_air
+ - mass_fraction_of_hydrophilic_black_carbon_in_air
+ - mass_fraction_of_hydrophobic_organic_carbon_in_air
+ - mass_fraction_of_hydrophilic_organic_carbon_in_air
+ - mass_fraction_of_dust001_in_air
+ - mass_fraction_of_dust002_in_air
+ - mass_fraction_of_dust003_in_air
+ - mass_fraction_of_dust004_in_air
+ - mass_fraction_of_dust005_in_air
+ - mass_fraction_of_sea_salt001_in_air
+ - mass_fraction_of_sea_salt002_in_air
+ - mass_fraction_of_sea_salt003_in_air
+ - mass_fraction_of_sea_salt004_in_air
+ - mass_fraction_of_sea_salt005_in_air
+
+{% set rescaling_factor_file = aero_rescaling_factor_file|default(aero_gen_bmatrix_rescale_default) %}
+{% include rescaling_factor_file %}
+
+number of halo points: {{ aero_diagb_n_halo }}
+number of neighbors: {{ aero_diagb_n_neighbors }}
+simple smoothing:
+ horizontal iterations: {{ aero_diagb_smooth_horiz_iter }}
+ vertical iterations: {{ aero_diagb_smooth_vert_iter }}
diff --git a/parm/jcb-gdas/algorithm/aero/aero_gen_bmatrix_diffusion.yaml.j2 b/parm/jcb-gdas/algorithm/aero/aero_gen_bmatrix_diffusion.yaml.j2
new file mode 100644
index 000000000..d1eaa28e2
--- /dev/null
+++ b/parm/jcb-gdas/algorithm/aero/aero_gen_bmatrix_diffusion.yaml.j2
@@ -0,0 +1,69 @@
+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_anl }}
+ npy: {{ aero_npy_anl }}
+ npz: {{ aero_npz_anl }}
+date: '{{ aero_background_error_time_iso }}'
+background:
+ datetime: '{{ aero_background_error_time_iso }}'
+ filetype: fms restart
+ state variables:
+ - mass_fraction_of_sulfate_in_air
+ - mass_fraction_of_hydrophobic_black_carbon_in_air
+ - mass_fraction_of_hydrophilic_black_carbon_in_air
+ - mass_fraction_of_hydrophobic_organic_carbon_in_air
+ - mass_fraction_of_hydrophilic_organic_carbon_in_air
+ - mass_fraction_of_dust001_in_air
+ - mass_fraction_of_dust002_in_air
+ - mass_fraction_of_dust003_in_air
+ - mass_fraction_of_dust004_in_air
+ - mass_fraction_of_dust005_in_air
+ - mass_fraction_of_sea_salt001_in_air
+ - mass_fraction_of_sea_salt002_in_air
+ - mass_fraction_of_sea_salt003_in_air
+ - mass_fraction_of_sea_salt004_in_air
+ - mass_fraction_of_sea_salt005_in_air
+ field io names:
+ mass_fraction_of_dust001_in_air: dust1
+ mass_fraction_of_dust002_in_air: dust2
+ mass_fraction_of_dust003_in_air: dust3
+ mass_fraction_of_dust004_in_air: dust4
+ mass_fraction_of_dust005_in_air: dust5
+ mass_fraction_of_sea_salt001_in_air: seas1
+ mass_fraction_of_sea_salt002_in_air: seas2
+ mass_fraction_of_sea_salt003_in_air: seas3
+ mass_fraction_of_sea_salt004_in_air: seas4
+ mass_fraction_of_sea_salt005_in_air: seas5
+ mass_fraction_of_hydrophobic_black_carbon_in_air: bc1
+ mass_fraction_of_hydrophilic_black_carbon_in_air: bc2
+ mass_fraction_of_hydrophobic_organic_carbon_in_air: oc1
+ mass_fraction_of_hydrophilic_organic_carbon_in_air: oc2
+ mass_fraction_of_sulfate_in_air: so4
+ datapath: {{ aero_background_path }}
+ filename_core: '{{ aero_background_error_time_fv3 }}.anlres.fv_core.res.nc'
+ filename_trcr: '{{ aero_background_error_time_fv3 }}.anlres.fv_tracer.res.nc'
+ filename_cplr: '{{ aero_background_error_time_fv3 }}.anlres.coupler.res'
+background error:
+ covariance model: SABER
+ saber central block:
+ saber block name: diffusion
+ calibration:
+ normalization:
+ iterations: {{ aero_diffusion_iter }}
+ groups:
+ - horizontal:
+ fixed value: {{ aero_diffusion_horiz_len }}
+ write:
+ filepath: "{{ aero_berror_diffusion_directory }}/diffusion_hz"
+ - vertical:
+ levels: {{ aero_npz_ges }}
+ fixed value: {{ aero_diffusion_fixed_val }}
+ as gaussian: true
+ write:
+ filepath: "{{ aero_berror_diffusion_directory }}/diffusion_vt"
diff --git a/parm/jcb-gdas/algorithm/aero/aero_gen_bmatrix_rescale_default.yaml.j2 b/parm/jcb-gdas/algorithm/aero/aero_gen_bmatrix_rescale_default.yaml.j2
new file mode 100644
index 000000000..55d14aebf
--- /dev/null
+++ b/parm/jcb-gdas/algorithm/aero/aero_gen_bmatrix_rescale_default.yaml.j2
@@ -0,0 +1,40 @@
+rescaling factors:
+ mass_fraction_of_sulfate_in_air:
+ rescaling factor: 0.1
+ mass_fraction_of_hydrophobic_black_carbon_in_air:
+ ocean rescaling factor: 1.0
+ land rescaling factor: 1.0
+ mass_fraction_of_hydrophilic_black_carbon_in_air:
+ ocean rescaling factor: 1.0
+ land rescaling factor: 1.0
+ mass_fraction_of_hydrophobic_organic_carbon_in_air:
+ ocean rescaling factor: 1.0
+ land rescaling factor: 1.0
+ mass_fraction_of_hydrophilic_organic_carbon_in_air:
+ ocean rescaling factor: 1.0
+ land rescaling factor: 1.0
+ mass_fraction_of_sea_salt001_in_air:
+ ocean rescaling factor: 1.0
+ land rescaling factor: 1.0
+ mass_fraction_of_sea_salt002_in_air:
+ ocean rescaling factor: 1.0
+ land rescaling factor: 1.0
+ mass_fraction_of_sea_salt003_in_air:
+ ocean rescaling factor: 1.0
+ land rescaling factor: 1.0
+ mass_fraction_of_sea_salt004_in_air:
+ ocean rescaling factor: 1.0
+ land rescaling factor: 1.0
+ mass_fraction_of_sea_salt005_in_air:
+ ocean rescaling factor: 1.0
+ land rescaling factor: 1.0
+ mass_fraction_of_dust001_in_air:
+ rescaling factor: 1.0
+ mass_fraction_of_dust002_in_air:
+ rescaling factor: 1.0
+ mass_fraction_of_dust003_in_air:
+ rescaling factor: 1.0
+ mass_fraction_of_dust004_in_air:
+ rescaling factor: 1.0
+ mass_fraction_of_dust005_in_air:
+ rescaling factor: 1.0
diff --git a/parm/jcb-gdas/algorithm/atmosphere/atm_addincrement.yaml.j2 b/parm/jcb-gdas/algorithm/atmosphere/atm_addincrement.yaml.j2
new file mode 100644
index 000000000..b11b3bdfc
--- /dev/null
+++ b/parm/jcb-gdas/algorithm/atmosphere/atm_addincrement.yaml.j2
@@ -0,0 +1,103 @@
+state geometry:
+ fms initialization:
+ namelist filename: ./fv3jedi/fmsmpp.nml
+ field table filename: ./fv3jedi/field_table
+ akbk: ./fv3jedi/akbk.nc4
+ layout:
+ - {{ atmosphere_layout_x }}
+ - {{ atmosphere_layout_y }}
+ npx: {{ atmosphere_npx_ges }}
+ npy: {{ atmosphere_npy_ges }}
+ npz: {{ atmosphere_npz_ges }}
+ field metadata override: ./fv3jedi/fv3jedi_fieldmetadata_history.yaml
+increment geometry:
+ fms initialization:
+ namelist filename: ./fv3jedi/fmsmpp.nml
+ field table filename: ./fv3jedi/field_table
+ akbk: ./fv3jedi/akbk.nc4
+ layout:
+ - {{ atmosphere_layout_x }}
+ - {{ atmosphere_layout_y }}
+ npx: {{ atmosphere_npx_anl }}
+ npy: {{ atmosphere_npy_anl }}
+ npz: {{ atmosphere_npz_anl }}
+ field metadata override: ./fv3jedi/fv3jedi_fieldmetadata_fv3inc.yaml
+state:
+ datetime: '{{ atmosphere_background_time_iso }}'
+ state variables:
+ - eastward_wind
+ - northward_wind
+ - water_vapor_mixing_ratio_wrt_moist_air
+ - cloud_liquid_ice
+ - cloud_liquid_water
+ - snow_water
+ - rain_water
+ - graupel
+ - ozone_mass_mixing_ratio
+ - air_pressure_thickness
+ - layer_thickness
+ field io names:
+ eastward_wind: ugrd
+ northward_wind: vgrd
+ air_temperature: tmp
+ water_vapor_mixing_ratio_wrt_moist_air: spfh
+ cloud_liquid_ice: icmr
+ cloud_liquid_water: clwmr
+ snow_water: snmr
+ rain_water: rwmr
+ graupel: grle
+ ozone_mass_mixing_ratio: o3mr
+ air_pressure_thickness: dpres
+ layer_thickness: delz
+ filetype: cube sphere history
+ provider: ufs
+ filename: {{ atmosphere_variational_history_prefix }}cubed_sphere_grid_atmf006.nc
+ datapath: ./
+ max allowable geometry difference: 1e-4
+increment:
+ added variables:
+ - eastward_wind
+ - northward_wind
+ - water_vapor_mixing_ratio_wrt_moist_air
+ - cloud_liquid_ice
+ - cloud_liquid_water
+ - snow_water
+ - rain_water
+ - graupel
+ - ozone_mass_mixing_ratio
+ - air_pressure_thickness
+ - layer_thickness
+ field io names:
+ eastward_wind: u_inc
+ northward_wind: v_inc
+ air_temperature: T_inc
+ water_vapor_mixing_ratio_wrt_moist_air: sphum_inc
+ cloud_liquid_ice: icmr_inc
+ cloud_liquid_water: liq_wat_inc
+ snow_water: snmr_inc
+ rain_water: rwmr_inc
+ graupel: grle_inc
+ ozone_mass_mixing_ratio: o3mr_inc
+ air_pressure_thickness: delp_inc
+ layer_thickness: delz_inc
+ filetype: fms restart
+ is restart: false
+ filename_nonrestart: {{ atmosphere_variational_analysis_prefix }}cubed_sphere_grid_atminc.nc
+ datapath: ./
+output:
+ filetype: auxgrid
+ gridtype: gaussian
+ filename: atmanl.
+ field io names:
+ eastward_wind: ugrd
+ northward_wind: vgrd
+ air_temperature: tmp
+ water_vapor_mixing_ratio_wrt_moist_air: spfh
+ cloud_liquid_ice: icmr
+ cloud_liquid_water: clwmr
+ snow_water: snmr
+ rain_water: rwmr
+ graupel: grle
+ ozone_mass_mixing_ratio: o3mr
+ air_pressure_thickness: dpres
+ layer_thickness: delz
diff --git a/parm/jcb-gdas/algorithm/atmosphere/fv3jedi_correction_increment.yaml.j2 b/parm/jcb-gdas/algorithm/atmosphere/fv3jedi_correction_increment.yaml.j2
new file mode 100644
index 000000000..170392af0
--- /dev/null
+++ b/parm/jcb-gdas/algorithm/atmosphere/fv3jedi_correction_increment.yaml.j2
@@ -0,0 +1,121 @@
+increment variables:
+- cloud_liquid_water
+- layer_thickness
+- air_pressure_thickness
+- cloud_liquid_ice
+- snow_water
+- rain_water
+- graupel
+- ozone_mass_mixing_ratio
+- water_vapor_mixing_ratio_wrt_moist_air
+- air_temperature
+- eastward_wind
+- northward_wind
+deterministic background geometry:
+ fms initialization:
+ namelist filename: ./fv3jedi/fmsmpp.nml
+ field table filename: ./fv3jedi/field_table
+ akbk: ./fv3jedi/akbk.nc4
+ layout:
+ - {{ atmosphere_layout_x }}
+ - {{ atmosphere_layout_y }}
+ npx: {{ atmosphere_npx_ges }}
+ npy: {{ atmosphere_npy_ges }}
+ npz: {{ atmosphere_npz_ges }}
+variational increment geometry:
+ fms initialization:
+ namelist filename: ./fv3jedi/fmsmpp.nml
+ field table filename: ./fv3jedi/field_table
+ akbk: ./fv3jedi/akbk.nc4
+ layout:
+ - {{ atmosphere_layout_x }}
+ - {{ atmosphere_layout_y }}
+ npx: {{ atmosphere_npx_anl }}
+ npy: {{ atmosphere_npy_anl }}
+ npz: {{ atmosphere_npz_anl }}
+ensemble mean analysis geometry:
+ fms initialization:
+ namelist filename: ./fv3jedi/fmsmpp.nml
+ field table filename: ./fv3jedi/field_table
+ akbk: ./fv3jedi/akbk.nc4
+ layout:
+ - {{ atmosphere_layout_x }}
+ - {{ atmosphere_layout_y }}
+ npx: {{ atmosphere_npx_anl }}
+ npy: {{ atmosphere_npy_anl }}
+ npz: {{ atmosphere_npz_anl }}
+correction increment geometry:
+ fms initialization:
+ namelist filename: ./fv3jedi/fmsmpp.nml
+ field table filename: ./fv3jedi/field_table
+ akbk: ./fv3jedi/akbk.nc4
+ layout:
+ - {{ atmosphere_layout_x }}
+ - {{ atmosphere_layout_y }}
+ npx: {{ atmosphere_npx_anl }}
+ npy: {{ atmosphere_npy_anl }}
+ npz: {{ atmosphere_npz_anl }}
+forecast hours:
+{% for ihour in range( atmosphere_iau_hours | length ) %}
+- datetime: '{{ atmosphere_iau_times_iso[ihour] }}'
+ deterministic background:
+ filetype: cube sphere history
+ provider: ufs
+ datapath: ./
+ filename: {{ atmosphere_variational_history_prefix }}cubed_sphere_grid_atmf{{ '%03d' % atmosphere_iau_hours[ihour] }}.nc
+ max allowable geometry difference: 1e-04
+ field io names:
+ eastward_wind: ugrd
+ northward_wind: vgrd
+ air_temperature: tmp
+ water_vapor_mixing_ratio_wrt_moist_air: spfh
+ cloud_liquid_ice: icmr
+ cloud_liquid_water: clwmr
+ snow_water: snmr
+ rain_water: rwmr
+ graupel: grle
+ ozone_mass_mixing_ratio: o3mr
+ air_pressure_thickness: dpres
+ layer_thickness: delz
+ variational increment:
+ filetype: fms restart
+ is restart: false
+ datapath: ./
+ filename_nonrestart: {{ atmosphere_variational_analysis_prefix }}cubed_sphere_grid_atmi{{ '%03d' % atmosphere_iau_hours[ihour] }}.nc
+ field io names:
+ eastward_wind: u_inc
+ northward_wind: v_inc
+ air_temperature: T_inc
+ water_vapor_mixing_ratio_wrt_moist_air: sphum_inc
+ cloud_liquid_ice: icmr_inc
+ cloud_liquid_water: liq_wat_inc
+ snow_water: snmr_inc
+ rain_water: rwmr_inc
+ graupel: grle_inc
+ ozone_mass_mixing_ratio: o3mr_inc
+ air_pressure_thickness: delp_inc
+ layer_thickness: delz_inc
+ ensemble mean analysis:
+ filetype: cube sphere history
+ provider: ufs
+ datapath: ./
+ filename: {{ atmosphere_ensemble_analysis_prefix }}cubed_sphere_grid_atma{{ '%03d' % atmosphere_iau_hours[ihour] }}.ensmean.nc
+ correction increment:
+ filetype: cube sphere history
+ provider: ufs
+ datapath: ./
+ filename: {{ atmosphere_ensemble_analysis_prefix }}cubed_sphere_grid_catmi{{ '%03d' % atmosphere_iau_hours[ihour] }}.nc
+ field io names:
+ eastward_wind: u_inc
+ northward_wind: v_inc
+ air_temperature: T_inc
+ water_vapor_mixing_ratio_wrt_moist_air: sphum_inc
+ cloud_liquid_ice: icmr_inc
+ cloud_liquid_water: liq_wat_inc
+ snow_water: snmr_inc
+ rain_water: rwmr_inc
+ graupel: grle_inc
+ ozone_mass_mixing_ratio: o3mr_inc
+ air_pressure_thickness: delp_inc
+ layer_thickness: delz_inc
+{% endfor %}
diff --git a/parm/jcb-gdas/algorithm/atmosphere/fv3jedi_ensemble_recenter.yaml.j2 b/parm/jcb-gdas/algorithm/atmosphere/fv3jedi_ensemble_recenter.yaml.j2
new file mode 100644
index 000000000..f71b855ad
--- /dev/null
+++ b/parm/jcb-gdas/algorithm/atmosphere/fv3jedi_ensemble_recenter.yaml.j2
@@ -0,0 +1,109 @@
+members:
+{% for imember in range(atmosphere_number_ensemble_members) %}
+{% for ihour in range( atmosphere_iau_hours | length ) %}
+- state geometry:
+ fms initialization:
+ namelist filename: ./fv3jedi/fmsmpp.nml
+ field table filename: ./fv3jedi/field_table
+ akbk: ./fv3jedi/akbk.nc4
+ layout:
+ - {{ atmosphere_layout_x }}
+ - {{ atmosphere_layout_y }}
+ npx: {{ atmosphere_npx_anl }}
+ npy: {{ atmosphere_npy_anl }}
+ npz: {{ atmosphere_npz_anl }}
+ increment geometry:
+ fms initialization:
+ namelist filename: ./fv3jedi/fmsmpp.nml
+ field table filename: ./fv3jedi/field_table
+ akbk: ./fv3jedi/akbk.nc4
+ layout:
+ - {{ atmosphere_layout_x }}
+ - {{ atmosphere_layout_y }}
+ npx: {{ atmosphere_npx_anl }}
+ npy: {{ atmosphere_npy_anl }}
+ npz: {{ atmosphere_npz_anl }}
+ state:
+ datetime: '{{ atmosphere_iau_times_iso[ihour] }}'
+ state variables:
+ - eastward_wind
+ - northward_wind
+ - air_temperature
+ - water_vapor_mixing_ratio_wrt_moist_air
+ - cloud_liquid_ice
+ - cloud_liquid_water
+ - snow_water
+ - rain_water
+ - graupel
+ - ozone_mass_mixing_ratio
+ - air_pressure_thickness
+ - layer_thickness
+ field io names:
+ eastward_wind: u_inc
+ northward_wind: v_inc
+ air_temperature: T_inc
+ water_vapor_mixing_ratio_wrt_moist_air: sphum_inc
+ cloud_liquid_ice: icmr_inc
+ cloud_liquid_water: liq_wat_inc
+ snow_water: snmr_inc
+ rain_water: rwmr_inc
+ graupel: grle_inc
+ ozone_mass_mixing_ratio: o3mr_inc
+ air_pressure_thickness: delp_inc
+ layer_thickness: delz_inc
+ filetype: cube sphere history
+ provider: ufs
+ datapath: ./
+ filename: {{ atmosphere_ensemble_analysis_prefix }}cubed_sphere_grid_catmi{{ '%03d' % atmosphere_iau_hours[ihour] }}.nc
+ max allowable geometry difference: 1e-4
+ increment:
+ added variables:
+ - eastward_wind
+ - northward_wind
+ - air_temperature
+ - water_vapor_mixing_ratio_wrt_moist_air
+ - cloud_liquid_ice
+ - cloud_liquid_water
+ - snow_water
+ - rain_water
+ - graupel
+ - ozone_mass_mixing_ratio
+ - air_pressure_thickness
+ - layer_thickness
+ field io names:
+ eastward_wind: u_inc
+ northward_wind: v_inc
+ air_temperature: T_inc
+ water_vapor_mixing_ratio_wrt_moist_air: sphum_inc
+ cloud_liquid_ice: icmr_inc
+ cloud_liquid_water: liq_wat_inc
+ snow_water: snmr_inc
+ rain_water: rwmr_inc
+ graupel: grle_inc
+ ozone_mass_mixing_ratio: o3mr_inc
+ air_pressure_thickness: delp_inc
+ layer_thickness: delz_inc
+ filetype: cube sphere history
+ provider: ufs
+ datapath: ./mem{{ '%0{}d'.format(3)|format(imember+1) }}
+ filename: {{ atmosphere_ensemble_analysis_prefix }}cubed_sphere_grid_atmi{{ '%03d' % atmosphere_iau_hours[ihour] }}.nc
+ output:
+ filetype: fms restart
+ is restart: false
+ datapath: ./mem{{ '%0{}d'.format(3)|format(imember+1) }}
+ filename_nonrestart: {{ atmosphere_ensemble_analysis_prefix }}cubed_sphere_grid_ratmi{{ '%03d' % atmosphere_iau_hours[ihour] }}.nc
+ field io names:
+ eastward_wind: u_inc
+ northward_wind: v_inc
+ air_temperature: T_inc
+ water_vapor_mixing_ratio_wrt_moist_air: sphum_inc
+ cloud_liquid_ice: icmr_inc
+ cloud_liquid_water: liq_wat_inc
+ snow_water: snmr_inc
+ rain_water: rwmr_inc
+ graupel: grle_inc
+ ozone_mass_mixing_ratio: o3mr_inc
+ air_pressure_thickness: delp_inc
+ layer_thickness: delz_inc
+{% endfor %}
+{% endfor %}
diff --git a/parm/jcb-gdas/algorithm/atmosphere/fv3jedi_fv3inc_lgetkf.yaml.j2 b/parm/jcb-gdas/algorithm/atmosphere/fv3jedi_fv3inc_lgetkf.yaml.j2
new file mode 100644
index 000000000..9cf1fb727
--- /dev/null
+++ b/parm/jcb-gdas/algorithm/atmosphere/fv3jedi_fv3inc_lgetkf.yaml.j2
@@ -0,0 +1,152 @@
+variable change:
+ variable change name: Model2GeoVaLs
+ input variables: &bkgvars
+ - eastward_wind
+ - northward_wind
+ - air_temperature
+ - air_pressure_at_surface
+ - water_vapor_mixing_ratio_wrt_moist_air
+ - cloud_liquid_ice
+ - cloud_liquid_water
+ - snow_water
+ - rain_water
+ - graupel
+ - ozone_mass_mixing_ratio
+ - geopotential_height_at_surface
+ output variables: &fv3incrvars
+ - eastward_wind
+ - northward_wind
+ - air_temperature
+ - water_vapor_mixing_ratio_wrt_moist_air
+ - cloud_liquid_ice
+ - cloud_liquid_water
+ - snow_water
+ - rain_water
+ - graupel
+ - ozone_mass_mixing_ratio
+ - air_pressure_thickness
+ - layer_thickness
+jedi increment variables:
+- eastward_wind
+- northward_wind
+- air_temperature
+- air_pressure_at_surface
+- water_vapor_mixing_ratio_wrt_moist_air
+- cloud_liquid_ice
+- cloud_liquid_water
+- snow_water
+- rain_water
+- graupel
+- ozone_mass_mixing_ratio
+fv3 increment variables: *fv3incrvars
+background geometry:
+ fms initialization:
+ namelist filename: ./fv3jedi/fmsmpp.nml
+ field table filename: ./fv3jedi/field_table
+ akbk: ./fv3jedi/akbk.nc4
+ layout:
+ - {{ atmosphere_layout_x }}
+ - {{ atmosphere_layout_y }}
+ npx: {{ atmosphere_npx_ges }}
+ npy: {{ atmosphere_npy_ges }}
+ npz: {{ atmosphere_npz_ges }}
+jedi increment geometry:
+ fms initialization:
+ namelist filename: ./fv3jedi/fmsmpp.nml
+ field table filename: ./fv3jedi/field_table
+ akbk: ./fv3jedi/akbk.nc4
+ layout:
+ - {{ atmosphere_layout_x }}
+ - {{ atmosphere_layout_y }}
+ npx: {{ atmosphere_npx_ges }}
+ npy: {{ atmosphere_npy_ges }}
+ npz: {{ atmosphere_npz_ges }}
+fv3 increment geometry:
+ fms initialization:
+ namelist filename: ./fv3jedi/fmsmpp.nml
+ field table filename: ./fv3jedi/field_table
+ akbk: ./fv3jedi/akbk.nc4
+ layout:
+ - {{ atmosphere_layout_x }}
+ - {{ atmosphere_layout_y }}
+ npx: {{ atmosphere_npx_ges }}
+ npy: {{ atmosphere_npy_ges }}
+ npz: {{ atmosphere_npz_ges }}
+members from template:
+ template:
+ background input:
+ datapath: ./bkg/mem%mem%
+ filetype: cube sphere history
+ provider: ufs
+ filenames:
+ - {{ atmosphere_ensemble_history_prefix }}cubed_sphere_grid_atmf006.nc
+ - {{ atmosphere_ensemble_history_prefix }}cubed_sphere_grid_sfcf006.nc
+ max allowable geometry difference: 1e-4
+ datetime: '{{ atmosphere_background_time_iso }}'
+ state variables: *bkgvars
+ field io names: &field_io_names
+ eastward_wind: ugrd
+ northward_wind: vgrd
+ air_temperature: tmp
+ layer_thickness: delz
+ air_pressure_thickness: dpres
+ air_pressure_at_surface: pressfc
+ water_vapor_mixing_ratio_wrt_moist_air: spfh
+ cloud_liquid_ice: icmr
+ cloud_liquid_water: clwmr
+ snow_water: snmr
+ rain_water: rwmr
+ graupel: grle
+ ozone_mass_mixing_ratio: o3mr
+ geopotential_height_at_surface: hgtsfc
+ jedi increment input:
+ filetype: cube sphere history
+ provider: ufs
+ field io names: *field_io_names
+ datapath: ./anl/mem%mem%
+ filename: cubed_sphere_grid_atminc.jedi.nc
+ fv3 increment output:
+{% if atm_enkfonly | default(false) %}
+ filetype: fms restart
+ is restart: false
+ filename_nonrestart: {{ atmosphere_ensemble_analysis_prefix }}cubed_sphere_grid_atminc.nc
+{% else %}
+ filetype: cube sphere history
+ provider: ufs
+ filename: {{ atmosphere_ensemble_analysis_prefix }}cubed_sphere_grid_atminc.nc
+{% endif %}
+ datapath: ./anl/mem%mem%
+ field io names:
+ eastward_wind: u_inc
+ northward_wind: v_inc
+ air_temperature: T_inc
+ water_vapor_mixing_ratio_wrt_moist_air: sphum_inc
+ cloud_liquid_water: liq_wat_inc
+ ozone_mass_mixing_ratio: o3mr_inc
+ cloud_liquid_ice: icmr_inc
+ snow_water: snmr_inc
+ rain_water: rwmr_inc
+ graupel: grle_inc
+ air_pressure_thickness: delp_inc
+ layer_thickness: delz_inc
+ pattern: '%mem%'
+ nmembers: {{ atmosphere_number_ensemble_members }}
+ zero padding: 3
+
+# Optionally test the application
+{% if do_testing | default(false) %}
+test:
+ reference filename: {{test_reference_filename}}
+{% if test_output_filename is defined %}
+ test output filename: {{test_output_filename}}
+{% endif %}
+{% if log_output_filename is defined %}
+ log output filename: {{log_output_filename}}
+{% endif %}
+{% if mpi_pattern is defined %}
+ mpi pattern: {{mpi_pattern}}
+{% endif %}
+ float relative tolerance: {{test_float_relative_tolerance | default(1.0e-6, true)}}
+ float absolute tolerance: {{test_float_absolute_tolerance | default(0.0, true) }}
+ integer tolerance: {{test_integer_tolerance | default(0, true) }}
+{% endif %}
diff --git a/parm/jcb-gdas/algorithm/atmosphere/fv3jedi_fv3inc_variational.yaml.j2 b/parm/jcb-gdas/algorithm/atmosphere/fv3jedi_fv3inc_variational.yaml.j2
new file mode 100644
index 000000000..40da72655
--- /dev/null
+++ b/parm/jcb-gdas/algorithm/atmosphere/fv3jedi_fv3inc_variational.yaml.j2
@@ -0,0 +1,147 @@
+variable change:
+ variable change name: Model2GeoVaLs
+ input variables: &bkgvars
+ - eastward_wind
+ - northward_wind
+ - air_temperature
+ - air_pressure_at_surface
+ - water_vapor_mixing_ratio_wrt_moist_air
+ - cloud_liquid_ice
+ - cloud_liquid_water
+ - ozone_mass_mixing_ratio
+ - snow_water
+ - rain_water
+ - graupel
+ - geopotential_height_at_surface
+ output variables: &fv3incrvars
+ - eastward_wind
+ - northward_wind
+ - air_temperature
+ - water_vapor_mixing_ratio_wrt_moist_air
+ - cloud_liquid_ice
+ - cloud_liquid_water
+ - snow_water
+ - rain_water
+ - graupel
+ - ozone_mass_mixing_ratio
+ - air_pressure_thickness
+ - layer_thickness
+jedi increment variables:
+- eastward_wind
+- northward_wind
+- air_temperature
+- air_pressure_at_surface
+- water_vapor_mixing_ratio_wrt_moist_air
+- cloud_liquid_ice
+- cloud_liquid_water
+- snow_water
+- rain_water
+- graupel
+- ozone_mass_mixing_ratio
+fv3 increment variables: *fv3incrvars
+background geometry:
+ fms initialization:
+ namelist filename: ./fv3jedi/fmsmpp.nml
+ field table filename: ./fv3jedi/field_table
+ akbk: ./fv3jedi/akbk.nc4
+ layout:
+ - {{ atmosphere_layout_x }}
+ - {{ atmosphere_layout_y }}
+ npx: {{ atmosphere_npx_ges }}
+ npy: {{ atmosphere_npy_ges }}
+ npz: {{ atmosphere_npz_ges }}
+jedi increment geometry:
+ fms initialization:
+ namelist filename: ./fv3jedi/fmsmpp.nml
+ field table filename: ./fv3jedi/field_table
+ akbk: ./fv3jedi/akbk.nc4
+ layout:
+ - {{ atmosphere_layout_x }}
+ - {{ atmosphere_layout_y }}
+ npx: {{ atmosphere_npx_his }}
+ npy: {{ atmosphere_npy_his }}
+ npz: {{ atmosphere_npz_his }}
+fv3 increment geometry:
+ fms initialization:
+ namelist filename: ./fv3jedi/fmsmpp.nml
+ field table filename: ./fv3jedi/field_table
+ akbk: ./fv3jedi/akbk.nc4
+ layout:
+ - {{ atmosphere_layout_x }}
+ - {{ atmosphere_layout_y }}
+ npx: {{ atmosphere_npx_his }}
+ npy: {{ atmosphere_npy_his }}
+ npz: {{ atmosphere_npz_his }}
+members:
+- background input:
+ datapath: ./bkg
+ filetype: cube sphere history
+ provider: ufs
+ datetime: "{{ atmosphere_background_time_iso }}"
+ filenames:
+ - {{ atmosphere_variational_history_prefix }}cubed_sphere_grid_atmf006.nc
+ - {{ atmosphere_variational_history_prefix }}cubed_sphere_grid_sfcf006.nc
+ max allowable geometry difference: 1e-4
+ state variables: *bkgvars
+ field io names: &field_io_names
+ eastward_wind: ugrd
+ northward_wind: vgrd
+ air_temperature: tmp
+ layer_thickness: delz
+ air_pressure_thickness: dpres
+ air_pressure_at_surface: pressfc
+ water_vapor_mixing_ratio_wrt_moist_air: spfh
+ cloud_liquid_ice: icmr
+ cloud_liquid_water: clwmr
+ snow_water: snmr
+ rain_water: rwmr
+ graupel: grle
+ ozone_mass_mixing_ratio: o3mr
+ geopotential_height_at_surface: hgtsfc
+ jedi increment input:
+ filetype: cube sphere history
+ provider: ufs
+ field io names: *field_io_names
+ datapath: ./anl
+ filename: cubed_sphere_grid_atminc.jedi.nc
+ fv3 increment output:
+{% if atmosphere_variational_increment_type == 'gaussian' %}
+ filetype: auxgrid
+ gridtype: gaussian
+ filename: ./anl/atminc.
+{% else %}
+ filetype: fms restart
+ is restart: false
+ datapath: ./anl
+ filename_nonrestart: {{ atmosphere_variational_analysis_prefix }}cubed_sphere_grid_atminc.nc
+{% endif %}
+ field io names:
+ eastward_wind: u_inc
+ northward_wind: v_inc
+ air_temperature: T_inc
+ water_vapor_mixing_ratio_wrt_moist_air: sphum_inc
+ cloud_liquid_water: liq_wat_inc
+ ozone_mass_mixing_ratio: o3mr_inc
+ cloud_liquid_ice: icmr_inc
+ snow_water: snmr_inc
+ rain_water: rwmr_inc
+ graupel: grle_inc
+ air_pressure_thickness: delp_inc
+ layer_thickness: delz_inc
+# Optionally test the application
+{% if do_testing | default(false) %}
+test:
+ reference filename: {{test_reference_filename}}
+{% if test_output_filename is defined %}
+ test output filename: {{test_output_filename}}
+{% endif %}
+{% if log_output_filename is defined %}
+ log output filename: {{log_output_filename}}
+{% endif %}
+{% if mpi_pattern is defined %}
+ mpi pattern: {{mpi_pattern}}
+{% endif %}
+ float relative tolerance: {{test_float_relative_tolerance | default(1.0e-6, true)}}
+ float absolute tolerance: {{test_float_absolute_tolerance | default(0.0, true) }}
+ integer tolerance: {{test_integer_tolerance | default(0, true) }}
+{% endif %}
diff --git a/parm/jcb-gdas/algorithm/marine/soca_chgres.yaml.j2 b/parm/jcb-gdas/algorithm/marine/soca_chgres.yaml.j2
new file mode 100644
index 000000000..2f417bc29
--- /dev/null
+++ b/parm/jcb-gdas/algorithm/marine/soca_chgres.yaml.j2
@@ -0,0 +1,33 @@
+input geometry:
+ mom6_input_nml: mom_input.nml
+ fields metadata: ./fields_metadata.yaml
+
+output geometry:
+ geom_grid_file: ./anl_geom/soca_gridspec.nc
+ mom6_input_nml: ./anl_geom/mom_input.nml
+ fields metadata: ./fields_metadata.yaml
+
+states:
+- input:
+ date: '{{ marine_window_end_iso }}'
+ basename: ./bkg/
+ ocn_filename: 'ocean.bkg.f009.nc'
+ ice_filename: 'ice.bkg.f009.nc'
+ read_from_file: 1
+
+ state variables:
+ - sea_surface_height_above_geoid
+ - sea_water_potential_temperature
+ - sea_water_salinity
+ - sea_water_cell_thickness
+ - sea_water_depth
+ - mom6_mld
+ - sea_ice_area_fraction
+ - sea_ice_thickness
+ - sea_ice_snow_thickness
+
+ output:
+ datadir: anl_geom/
+ exp: f009_anl_geom
+ type: fc
+ date: '{{ marine_window_end_iso }}'
\ No newline at end of file
diff --git a/parm/jcb-gdas/algorithm/marine/soca_diag_stats.yaml.j2 b/parm/jcb-gdas/algorithm/marine/soca_diag_stats.yaml.j2
new file mode 100644
index 000000000..8c774648c
--- /dev/null
+++ b/parm/jcb-gdas/algorithm/marine/soca_diag_stats.yaml.j2
@@ -0,0 +1,18 @@
+time window:
+ begin: '1900-01-01T00:00:00Z'
+ end: '2035-01-01T00:00:00Z'
+ bound to include: begin
+cycle date: {{ marine_window_middle_iso }}
+obs spaces:
+{% for observation_from_jcb in cleaned_observations %}
+- obs space:
+ name: '{{ observation_from_jcb }}'
+ obsdatain:
+ engine:
+ type: H5File
+ obsfile: "{{ marine_obsdataout_path }}/{{ marine_obsdataout_prefix }}{{ observation_from_jcb }}{{ marine_obsdataout_suffix }}"
+ simulated variables: ['{{ obs_variables[observation_from_jcb] }}']
+ variable: '{{ obs_variables[observation_from_jcb] }}'
+ experiment identifier: '{{ pslot }}'
+ csv output: '{{marine_obsdataout_path}}/{{ marine_obsdatain_prefix }}ocn.{{ observation_from_jcb }}.stats.csv'
+{% endfor %}
diff --git a/parm/jcb-gdas/algorithm/marine/soca_diagb.yaml.j2 b/parm/jcb-gdas/algorithm/marine/soca_diagb.yaml.j2
new file mode 100644
index 000000000..8be8b26d5
--- /dev/null
+++ b/parm/jcb-gdas/algorithm/marine/soca_diagb.yaml.j2
@@ -0,0 +1,51 @@
+geometry:
+ mom6_input_nml: mom_input.nml
+ fields metadata: ./fields_metadata.yaml
+
+output geometry:
+ geom_grid_file: ./anl_geom/soca_gridspec.nc
+ mom6_input_nml: ./anl_geom/mom_input.nml
+ fields metadata: ./fields_metadata.yaml
+
+date: '{{ marine_window_end_iso }}'
+
+background:
+ date: '{{ marine_window_end_iso }}'
+ 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_iso }}'
+ exp: bkgerr_parametric_stddev
+ type: incr
+
+variables:
+ name:
+ - sea_water_potential_temperature
+ - sea_water_salinity
+# - eastward_sea_water_velocity
+# - northward_sea_water_velocity
+ - sea_water_cell_thickness
+ - sea_surface_height_above_geoid
+ - sea_ice_area_fraction
+ - sea_ice_thickness
+ - sea_ice_snow_thickness
+# - mom6_mld
+
+
+vertical e-folding scale dynamic: 200.0
+vertical e-folding scale static: 300.0
+stencil growth iterations: 100
+min efold depth ratio: 3.0
+rescale dynamic: 0.2
+rescale static: 1.0
+static sig B:
+ sigT: 0.5
+ sigS: 0.1
+ sigSic: 0.01
+max ssh: 0.0
+min depth: 100.0
+vertical bin size: 1.0
diff --git a/parm/jcb-gdas/algorithm/marine/soca_diags_finalize.yaml.j2 b/parm/jcb-gdas/algorithm/marine/soca_diags_finalize.yaml.j2
new file mode 100644
index 000000000..a05143b34
--- /dev/null
+++ b/parm/jcb-gdas/algorithm/marine/soca_diags_finalize.yaml.j2
@@ -0,0 +1,8 @@
+copy_opt:
+{% for observation_from_jcb in observations %}
+{% if use_observer(observation_from_jcb) %}
+- ['{{marine_obsdataout_path}}/{{observation_from_jcb}}{{marine_obsdataout_suffix}}', '{{marine_obsdatastats_path}}']
+- ['{{marine_obsdataout_path}}/{{marine_obsdatain_prefix}}ocn.{{observation_from_jcb}}.stats.csv', '{{marine_obsdatastats_path}}']
+{% endif %}
+{% endfor %}
+- ['{{marine_output_dir}}/soca_diag_stats.yaml', '{{marine_config_path}}']
diff --git a/parm/jcb-gdas/algorithm/marine/soca_ens_handler.yaml.j2 b/parm/jcb-gdas/algorithm/marine/soca_ens_handler.yaml.j2
new file mode 100644
index 000000000..764a5b995
--- /dev/null
+++ b/parm/jcb-gdas/algorithm/marine/soca_ens_handler.yaml.j2
@@ -0,0 +1,110 @@
+# This yaml is for applying deterministic recentering increments to the ensemble members
+geometry:
+ mom6_input_nml: mom_input.nml
+ fields metadata: ./fields_metadata.yaml
+
+nens: '{{ marine_number_ensemble_members }}'
+nens per MPI task: '{{ marine_number_ensemble_members_per_mpi }}'
+
+increment variables: &vars
+- sea_water_potential_temperature
+- sea_water_salinity
+- eastward_sea_water_velocity
+- northward_sea_water_velocity
+- sea_ice_area_fraction
+- sea_ice_thickness
+- sea_ice_snow_thickness
+
+backgrounds:
+ members from template:
+ nmembers: '{{ marine_number_ensemble_members }}'
+ pattern: "%mem%"
+ template:
+ date: "{{ marine_window_end_iso }}"
+ basename: ./ens/
+ ocn_filename: "ocean.%mem%.nc"
+ ice_filename: "ice.%mem%.nc"
+ read_from_file: 1
+ state variables:
+ - sea_water_potential_temperature
+ - sea_water_salinity
+ - sea_water_cell_thickness
+ - eastward_sea_water_velocity
+ - northward_sea_water_velocity
+ - sea_ice_area_fraction
+ - sea_ice_thickness
+ - sea_ice_snow_thickness
+
+recentering state:
+ state variables:
+ - sea_water_potential_temperature
+ - sea_water_salinity
+ - eastward_sea_water_velocity
+ - northward_sea_water_velocity
+ - sea_water_cell_thickness
+ - sea_water_depth
+ - ocean_mixed_layer_thickness
+ - sea_ice_area_fraction
+ - sea_ice_thickness
+ - sea_ice_snow_thickness
+ date: "{{ marine_window_end_iso }}"
+ basename: ./bkg/
+ ocn_filename: ocean.bkg.f009.nc
+ ice_filename: ice.bkg.f009.nc
+ read_from_file: 1
+
+output increments:
+ datadir: ./
+ date: "{{ marine_window_end_iso }}"
+ exp: recenter
+ type: ens
+
+increment postprocessing:
+ append vertical geometry:
+ layers variable: sea_water_cell_thickness
+ vertical geometry:
+ date: "{{ marine_window_begin_iso }}"
+ basename: ./INPUT/
+ ocn_filename: MOM.res.nc
+ read_from_file: 3
+ set increment variables to zero:
+ - eastward_sea_water_velocity
+ - northward_sea_water_velocity
+
+analysis postprocessing:
+ sea ice variable change:
+ variable change name: Soca2Cice
+ pattern: "%mem%"
+ arctic:
+ seaice edge: 0.4
+ shuffle: true
+ rescale prior:
+ rescale: true
+ min hice: 0.5
+ min hsno: 0.1
+ antarctic:
+ seaice edge: 0.4
+ shuffle: true
+ rescale prior:
+ rescale: true
+ min hice: 0.5
+ min hsno: 0.1
+ cice background state:
+ restart: ens/cice_model.res.%mem%.nc
+ ncat: 5
+ ice_lev: 7
+ sno_lev: 1
+ cice output:
+ restart: ens/cice_model.res.%mem%.nc
+ output variables:
+ - sea_water_potential_temperature
+ - sea_water_salinity
+ - sea_ice_area_fraction
+ - sea_ice_thickness
+ - sea_ice_snow_thickness
+
+ensemble variance output:
+ datadir: ./
+ date: "{{ marine_window_end_iso }}"
+ exp: ensvar
+ type: incr
diff --git a/parm/jcb-gdas/algorithm/marine/soca_ensb.yaml.j2 b/parm/jcb-gdas/algorithm/marine/soca_ensb.yaml.j2
new file mode 100644
index 000000000..9351877c7
--- /dev/null
+++ b/parm/jcb-gdas/algorithm/marine/soca_ensb.yaml.j2
@@ -0,0 +1,122 @@
+# Configuration for the recentering and re-balancing of the ensemble members
+geometry:
+ mom6_input_nml: mom_input.nml
+ fields metadata: ./fields_metadata.yaml
+
+output geometry:
+ geom_grid_file: ./anl_geom/soca_gridspec.nc
+ mom6_input_nml: ./anl_geom/mom_input.nml
+ fields metadata: ./fields_metadata.yaml
+
+date: '{{ marine_window_begin_iso }}'
+
+layers variable: [sea_water_cell_thickness]
+
+increment variables:
+- sea_water_potential_temperature
+- sea_water_salinity
+- eastward_sea_water_velocity
+- northward_sea_water_velocity
+- sea_surface_height_above_geoid
+- sea_water_cell_thickness
+- sea_ice_area_fraction
+- sea_ice_thickness
+- sea_ice_snow_thickness
+
+set increment variables to zero: [sea_surface_height_above_geoid]
+
+vertical geometry:
+ date: '{{ marine_window_begin_iso }}'
+ 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: '{{ marine_number_ensemble_members }}'
+ pattern: '%mem%'
+ template:
+ date: '{{ marine_window_begin_iso }}'
+ basename: '{{ marine_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_iso }}'
+ exp: ens_mean
+ type: incr
+
+ssh output:
+ unbalanced:
+ datadir: ./staticb/
+ date: '{{ marine_window_begin_iso }}'
+ exp: ssh_unbal_stddev
+ type: incr
+
+ steric:
+ datadir: ./staticb/
+ date: '{{ marine_window_begin_iso }}'
+ exp: ssh_steric_stddev
+ type: incr
+
+ total:
+ datadir: ./staticb/
+ date: '{{ marine_window_begin_iso }}'
+ exp: ssh_total_stddev
+ type: incr
+
+ explained variance:
+ datadir: ./staticb/
+ date: '{{ marine_window_begin_iso }}'
+ exp: steric_explained_variance
+ type: incr
+
+ recentering error:
+ datadir: ./staticb/
+ date: '{{ marine_window_begin_iso }}'
+ exp: ssh_recentering_error
+ type: incr
+
+background error output:
+ datadir: ./staticb/
+ date: '{{ marine_window_begin_iso }}'
+ exp: bkgerr_ens_stddev
+ type: incr
+
+linear variable change:
+ linear variable changes:
+ - linear variable change name: BalanceSOCA
+
+trajectory:
+ state variables:
+ - sea_water_potential_temperature
+ - sea_water_salinity
+ - eastward_sea_water_velocity
+ - northward_sea_water_velocity
+ - sea_surface_height_above_geoid
+ - sea_water_cell_thickness
+ - sea_water_depth
+ - ocean_mixed_layer_thickness
+ - sea_ice_area_fraction
+ - sea_ice_thickness
+ - sea_ice_snow_thickness
+ date: '{{ marine_window_begin_iso }}'
+ basename: ./INPUT/
+ ocn_filename: MOM.res.nc
+ ice_filename: cice.res.nc
+ read_from_file: 1
+
+output increment:
+ datadir: '{{ marine_enspert_relpath }}/'
+ date: '{{ marine_window_begin_iso }}'
+ exp: trash
+ type: incr
+ output file: 'pert.%mem%.nc'
+ pattern: '%mem%'
diff --git a/parm/jcb-gdas/algorithm/marine/soca_ensweights.yaml.j2 b/parm/jcb-gdas/algorithm/marine/soca_ensweights.yaml.j2
new file mode 100644
index 000000000..00b2e1ef8
--- /dev/null
+++ b/parm/jcb-gdas/algorithm/marine/soca_ensweights.yaml.j2
@@ -0,0 +1,52 @@
+geometry:
+ mom6_input_nml: mom_input.nml
+ fields metadata: ./fields_metadata.yaml
+
+output geometry:
+ geom_grid_file: ./anl_geom/soca_gridspec.nc
+ mom6_input_nml: ./anl_geom/mom_input.nml
+ fields metadata: ./fields_metadata.yaml
+
+date: '{{ marine_window_middle_iso }}'
+
+variables:
+ ice:
+ - sea_ice_area_fraction
+ - sea_ice_thickness
+ - sea_ice_snow_thickness
+
+ ocean:
+ - sea_water_potential_temperature
+ - sea_water_salinity
+ - eastward_sea_water_velocity
+ - northward_sea_water_velocity
+ - sea_surface_height_above_geoid
+
+background:
+ date: '{{ marine_window_begin_iso }}'
+ 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
+ # Example below was for old ens. from Xiao
+ # 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_iso }}'
+ exp: ens_weights
+ type: incr
diff --git a/parm/jcb-gdas/algorithm/marine/soca_gridgen.yaml.j2 b/parm/jcb-gdas/algorithm/marine/soca_gridgen.yaml.j2
new file mode 100644
index 000000000..34fbdeca6
--- /dev/null
+++ b/parm/jcb-gdas/algorithm/marine/soca_gridgen.yaml.j2
@@ -0,0 +1,5 @@
+geometry:
+ geom_grid_file: soca_gridspec.nc
+ mom6_input_nml: mom_input.nml
+ fields metadata: fields_metadata.yaml
+ rossby file: rossrad.nc
diff --git a/parm/jcb-gdas/algorithm/marine/soca_incpostproc.yaml.j2 b/parm/jcb-gdas/algorithm/marine/soca_incpostproc.yaml.j2
new file mode 100644
index 000000000..a2f0c2ab9
--- /dev/null
+++ b/parm/jcb-gdas/algorithm/marine/soca_incpostproc.yaml.j2
@@ -0,0 +1,115 @@
+geometry:
+ mom6_input_nml: mom_input.nml
+ fields metadata: ./fields_metadata.yaml
+
+date: '{{ marine_window_begin_iso }}'
+
+layers variable: [sea_water_cell_thickness]
+
+domains: [ocn, ice]
+
+increment variables:
+- sea_water_potential_temperature
+- sea_water_salinity
+#- eastward_sea_water_velocity
+#- northward_sea_water_velocity
+- sea_surface_height_above_geoid # Not used in MOM6 iau
+- sea_ice_area_fraction
+- sea_ice_thickness
+- sea_ice_snow_thickness
+
+set increment variables to zero:
+- eastward_sea_water_velocity
+- northward_sea_water_velocity
+
+vertical geometry:
+ date: '{{ marine_window_begin_iso }}'
+ basename: ./INPUT/
+ ocn_filename: MOM.res.nc
+ read_from_file: 1
+
+soca increment:
+ date: '{{ marine_window_begin_iso }}'
+ basename: ./Data/
+ ocn_filename: 'ocn.3dvarfgat_pseudo.incr.{{ marine_window_middle_iso }}.nc'
+ ice_filename: 'ice.3dvarfgat_pseudo.incr.{{ marine_window_middle_iso }}.nc'
+ read_from_file: 1
+
+output increment:
+ datadir: ./
+ date: '{{ marine_window_begin_iso }}'
+ exp: mom6_iau
+ type: incr
+ output file: inc.nc
+
+increment precision:
+- field: sea_water_potential_temperature
+ precision: 1.e-7
+- field: sea_water_salinity
+ precision: 1.e-7
+- field: sea_surface_height_above_geoid # Not used in MOM6 iau
+ precision: 1.e-7
+- field: sea_ice_area_fraction
+ precision: 1.e-7
+
+qc increment:
+ state bounds:
+ sea_water_potential_temperature: [-2.5, 36.0]
+ sea_water_salinity: [0.0, 44.0]
+ increment max:
+ steric: 0.5
+ increment stability iterations: 20
+ min stable density gradient: 1e-4
+ steric increment:
+ linear variable changes:
+ - linear variable change name: BalanceSOCA
+
+soca background: # background at the beginning of the window, used to compute analysis at the beginning of the window for soca2cice
+ date: '{{ marine_window_begin_iso }}'
+ basename: ./INPUT/
+ ocn_filename: MOM.res.nc
+ ice_filename: cice.res.nc
+ read_from_file: 1
+ state variables:
+ - sea_water_potential_temperature
+ - sea_water_salinity
+ - sea_surface_height_above_geoid
+ - eastward_sea_water_velocity
+ - northward_sea_water_velocity
+ - ocean_mixed_layer_thickness
+ - sea_water_depth
+ - sea_water_cell_thickness
+ - sea_ice_area_fraction
+ - sea_ice_thickness
+ - sea_ice_snow_thickness
+
+ice analysis postprocessing:
+ variable change name: Soca2Cice
+ arctic:
+ seaice edge: 0.4
+ shuffle: true
+ rescale prior:
+ rescale: true
+ min hice: 0.5
+ min hsno: 0.1
+ antarctic:
+ seaice edge: 0.4
+ shuffle: true
+ rescale prior:
+ rescale: true
+ min hice: 0.5
+ min hsno: 0.1
+ cice background state:
+ restart: ./Data/{{ marine_cice_date_fms }}.cice_model.res.nc
+ ncat: 5
+ ice_lev: 7
+ sno_lev: 1
+ cice output:
+ restart: ./Data/{{ marine_cice_date_fms }}.cice_model.res.nc
+ output variables:
+ - sea_water_potential_temperature
+ - sea_water_salinity
+ - sea_ice_area_fraction
+ - sea_ice_thickness
+ - sea_ice_snow_thickness
+
diff --git a/parm/jcb-gdas/algorithm/marine/soca_parameters_diffusion_hz.yaml.j2 b/parm/jcb-gdas/algorithm/marine/soca_parameters_diffusion_hz.yaml.j2
new file mode 100644
index 000000000..cb57948ab
--- /dev/null
+++ b/parm/jcb-gdas/algorithm/marine/soca_parameters_diffusion_hz.yaml.j2
@@ -0,0 +1,43 @@
+# Analysis/B-mat resolution
+geometry: &geom
+ geom_grid_file: ./anl_geom/soca_gridspec.nc
+ mom6_input_nml: ./anl_geom/mom_input.nml
+ fields metadata: ./fields_metadata.yaml
+
+# Background interpolated at the analysis resolution
+background:
+ read_from_file: 1
+ basename: ./anl_geom/
+ ocn_filename: 'ocn.f009_anl_geom.fc.{{ marine_window_end_iso }}.PT0S.nc'
+ ice_filename: 'ice.f009_anl_geom.fc.{{ marine_window_end_iso }}.PT0S.nc'
+ date: '{{ marine_window_end_iso }}'
+ state variables: [sea_surface_height_above_geoid]
+
+background error:
+ covariance model: SABER
+ saber central block:
+ saber block name: diffusion
+ geometry: *geom
+ calibration:
+ normalization:
+ method: randomization
+ iterations: 1000
+
+ groups:
+ - horizontal:
+ model file:
+ date: '{{ marine_window_end_iso }}'
+ basename: ./
+ ocn_filename: ocn.cor_rh.incr.0001-01-01T00:00:00Z.nc
+ model variable: sea_surface_height_above_geoid
+ write:
+ filepath: ./staticb/hz_ocean
+
+# TODO(G): OK to not use what's below but it will need
+# to be fixed when we add ice thickness and
+# snow depth
+# - horizontal:
+# as gaussian: true
+# fixed value: 50000.0
+# write:
+# filepath: ./staticb/hz_ice
diff --git a/parm/jcb-gdas/algorithm/marine/soca_parameters_diffusion_vt.yaml.j2 b/parm/jcb-gdas/algorithm/marine/soca_parameters_diffusion_vt.yaml.j2
new file mode 100644
index 000000000..a5c5d4641
--- /dev/null
+++ b/parm/jcb-gdas/algorithm/marine/soca_parameters_diffusion_vt.yaml.j2
@@ -0,0 +1,36 @@
+# Analysis/B-mat resolution
+geometry: &geom
+ geom_grid_file: ./anl_geom/soca_gridspec.nc
+ mom6_input_nml: ./anl_geom/mom_input.nml
+ fields metadata: ./fields_metadata.yaml
+
+# Background interpolated at the analysis resolution
+background:
+ read_from_file: 1
+ basename: ./anl_geom/
+ ocn_filename: 'ocn.f009_anl_geom.fc.{{ marine_window_end_iso }}.PT0S.nc'
+ date: '{{ marine_window_end_iso }}'
+ state variables: [sea_water_potential_temperature]
+
+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
+ levels: '{{ marine_vt_levels }}'
+ model file:
+ date: '{{ marine_window_middle_iso }}'
+ basename: ./
+ ocn_filename: vt_scales.nc
+ model variable: sea_water_potential_temperature
+ write:
+ filepath: ./staticb/vt_ocean
diff --git a/parm/jcb-gdas/algorithm/marine/soca_setcorscales.yaml.j2 b/parm/jcb-gdas/algorithm/marine/soca_setcorscales.yaml.j2
new file mode 100644
index 000000000..d87f3371f
--- /dev/null
+++ b/parm/jcb-gdas/algorithm/marine/soca_setcorscales.yaml.j2
@@ -0,0 +1,30 @@
+resolution:
+ geom_grid_file: ./anl_geom/soca_gridspec.nc
+ mom6_input_nml: ./anl_geom/mom_input.nml
+ fields metadata: ./fields_metadata.yaml
+
+date: "0001-01-01T00:00:00Z"
+
+corr variables: [sea_surface_height_above_geoid]
+
+islands:
+ # Barrier Islands between the Pamlico Sound and the Atlantic
+ scale: 100.0 # in kilometers
+ lat: [ 34.636, 35.065, 35.49, 35.87, 36.28]
+ lon: [-76.52, -76.03, -75.46, -75.56, -75.78]
+
+scales:
+ vert layers: 5 # in units of layer
+ sea_surface_height_above_geoid:
+ rossby mult: 1.0
+ min grid mult: 1.0
+
+rh output:
+ datadir: ./
+ exp: cor_rh
+ type: incr
+
+rv output:
+ datadir: ./
+ exp: cor_rv
+ type: incr
diff --git a/parm/jcb-gdas/algorithm/marine/soca_vtscales.yaml.j2 b/parm/jcb-gdas/algorithm/marine/soca_vtscales.yaml.j2
new file mode 100644
index 000000000..f0e68bc15
--- /dev/null
+++ b/parm/jcb-gdas/algorithm/marine/soca_vtscales.yaml.j2
@@ -0,0 +1,13 @@
+gridspec_filename: ./anl_geom/soca_gridspec.nc
+restart_filename: './anl_geom/ocn.f009_anl_geom.fc.{{ marine_window_end_iso }}.PT0S.nc'
+mld_filename: './anl_geom/ocn.f009_anl_geom.fc.{{ marine_window_end_iso }}.PT0S.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
diff --git a/parm/jcb-gdas/algorithm/observation_statistics/anlstat.yaml.j2 b/parm/jcb-gdas/algorithm/observation_statistics/anlstat.yaml.j2
new file mode 100644
index 000000000..420544cce
--- /dev/null
+++ b/parm/jcb-gdas/algorithm/observation_statistics/anlstat.yaml.j2
@@ -0,0 +1,11 @@
+time window:
+ begin: '{{ current_cycle_iso }}'
+ length: '{{ window_length }}'
+ bound to include: '{{ bound_to_include | default("begin", true) }}'
+
+observers:
+{% for observation_from_jcb in observations %}
+{% filter indent(width=2) %}
+{% include observation_from_jcb + '.yaml.j2' %}
+{% endfilter %}
+{% endfor %}
diff --git a/parm/jcb-gdas/algorithm/snow/fv3jedi_land_ensrecenter.yaml.j2 b/parm/jcb-gdas/algorithm/snow/fv3jedi_land_ensrecenter.yaml.j2
new file mode 100644
index 000000000..5d1eb1630
--- /dev/null
+++ b/parm/jcb-gdas/algorithm/snow/fv3jedi_land_ensrecenter.yaml.j2
@@ -0,0 +1,94 @@
+geometry:
+ fms initialization:
+ namelist filename: ./fv3jedi/fmsmpp.nml
+ field table filename: ./fv3jedi/field_table
+ akbk: ./fv3jedi/akbk.nc4
+ layout:
+ - {{ layout_x }}
+ - {{ layout_y }}
+ npx: {{ npx_ges }}
+ npy: {{ npy_ges }}
+ npz: {{ npz_ges }}
+date: "{{ snow_background_time_iso }}"
+variables:
+- totalSnowDepth
+increment mask:
+ variable:
+ - slmsk
+ minvalue: 0.99
+ maxvalue: 1.01
+ background:
+ datetime: "{{ snow_background_time_iso }}"
+ filetype: fms restart
+ state variables:
+ - slmsk
+ datapath: ./bkg/mem001
+ filename is datetime templated: true
+ filename_core: "%yyyy%mm%dd.%hh%MM%ss.fv_core.res.nc"
+ filename_trcr: "%yyyy%mm%dd.%hh%MM%ss.fv_tracer.res.nc"
+ filename_sfcd: "%yyyy%mm%dd.%hh%MM%ss.sfc_data.nc"
+ filename_sfcw: "%yyyy%mm%dd.%hh%MM%ss.fv_srf_wnd.res.nc"
+ filename_cplr: "%yyyy%mm%dd.%hh%MM%ss.coupler.res"
+ skip coupler file: true
+deterministic increment:
+ datetime: "{{ snow_increment_time_iso }}"
+ filetype: fms restart
+ state variables:
+ - totalSnowDepth
+ field io names:
+ totalSnowDepth: snodl
+ datapath: ./inc/det_ensres
+ filename is datetime templated: true
+ filename_core: "snowinc.%yyyy%mm%dd.%hh%MM%ss.fv_core.res.nc"
+ filename_trcr: "snowinc.%yyyy%mm%dd.%hh%MM%ss.fv_tracer.res.nc"
+ filename_sfcd: "snowinc.%yyyy%mm%dd.%hh%MM%ss.sfc_data.nc"
+ filename_sfcw: "snowinc.%yyyy%mm%dd.%hh%MM%ss.fv_srf_wnd.res.nc"
+ filename_cplr: "snowinc.%yyyy%mm%dd.%hh%MM%ss.coupler.res"
+ skip coupler file: true
+deterministic background:
+ datetime: "{{ snow_background_time_iso }}"
+ filetype: fms restart
+ state variables:
+ - totalSnowDepth
+ field io names:
+ totalSnowDepth: snodl
+ datapath: ./bkg/det_ensres
+ filename is datetime templated: true
+ filename_core: "%yyyy%mm%dd.%hh%MM%ss.fv_core.res.nc"
+ filename_trcr: "%yyyy%mm%dd.%hh%MM%ss.fv_tracer.res.nc"
+ filename_sfcd: "%yyyy%mm%dd.%hh%MM%ss.sfc_data.nc"
+ filename_sfcw: "%yyyy%mm%dd.%hh%MM%ss.fv_srf_wnd.res.nc"
+ filename_cplr: "%yyyy%mm%dd.%hh%MM%ss.coupler.res"
+ skip coupler file: true
+recenter to: deterministic
+output increment:
+ datapath: ./inc/ensmean
+ datetime: "{{ snow_increment_time_iso }}"
+ filetype: fms restart
+ field io names:
+ totalSnowDepth: snodl
+ prefix: snowinc
+ filename_core: "{{ snow_increment_time_fv3 }}.fv_core.res.nc"
+ filename_trcr: "{{ snow_increment_time_fv3 }}.fv_tracer.res.nc"
+ filename_sfcd: "{{ snow_increment_time_fv3 }}.sfc_data.nc"
+ filename_sfcw: "{{ snow_increment_time_fv3 }}.fv_srf_wnd.res.nc"
+ filename_cplr: "{{ snow_increment_time_fv3 }}.coupler.res"
+ensemble backgrounds:
+ pattern: "{{ ensemble_pattern | default("%mem%", true) }}"
+ number of members: {{ number_ensemble_members }}
+ zero padding: 3
+ template:
+ datetime: "{{ snow_background_time_iso }}"
+ filetype: fms restart
+ state variables:
+ - totalSnowDepth
+ field io names:
+ totalSnowDepth: snodl
+ datapath: ./bkg/mem%mem%
+ filename is datetime templated: true
+ filename_core: "%yyyy%mm%dd.%hh%MM%ss.fv_core.res.nc"
+ filename_trcr: "%yyyy%mm%dd.%hh%MM%ss.fv_tracer.res.nc"
+ filename_sfcd: "%yyyy%mm%dd.%hh%MM%ss.sfc_data.nc"
+ filename_sfcw: "%yyyy%mm%dd.%hh%MM%ss.fv_srf_wnd.res.nc"
+ filename_cplr: "%yyyy%mm%dd.%hh%MM%ss.coupler.res"
+ skip coupler file: true
diff --git a/parm/jcb-gdas/algorithm/snow/fv3jedi_snow_ensmean.yaml.j2 b/parm/jcb-gdas/algorithm/snow/fv3jedi_snow_ensmean.yaml.j2
new file mode 100644
index 000000000..9bd29e33a
--- /dev/null
+++ b/parm/jcb-gdas/algorithm/snow/fv3jedi_snow_ensmean.yaml.j2
@@ -0,0 +1,49 @@
+geometry:
+{% filter indent(width=2) %}
+{% set geometry_background_file = geometry_background_file|default(model_component ~ 'geometry_background', true) ~ '.yaml.j2' %}
+{% include geometry_background_file %}
+{% endfilter %}
+mean output:
+ filetype: fms restart
+ datapath: ./bkg/ensmean
+ filename_core: fv_core.res.nc
+ filename_trcr: fv_tracer.res.nc
+ filename_sfcd: sfc_data.nc
+ filename_sfcw: fv_srf_wnd.res.nc
+ filename_cplr: coupler.res
+ state variables:
+ - totalSnowDepth
+ - vtype
+ - slmsk
+ - filtered_orography
+ - stc
+ - sheleg
+ - fraction_of_ice
+ field io names:
+ totalSnowDepth: snodl
+ filtered_orography: orog_filt
+ fraction_of_ice: fice
+ensemble:
+ members from template:
+ template:
+ datetime: '{{ snow_background_time_iso }}'
+ filetype: fms restart
+ state variables:
+ - totalSnowDepth
+ - vtype
+ - slmsk
+ - filtered_orography
+ - stc
+ - sheleg
+ - fraction_of_ice
+ field io names:
+ totalSnowDepth: snodl
+ filtered_orography: orog_filt
+ fraction_of_ice: fice
+ datapath: ./bkg/mem%mem%/
+ filename_sfcd: '{{ snow_background_time_fv3 }}.sfc_data.nc'
+ filename_cplr: '{{ snow_background_time_fv3 }}.coupler.res'
+ filename_orog: '{{ snow_orog_prefix }}_oro_data.nc'
+ pattern: '%mem%'
+ nmembers: {{ snow_number_ensemble_members }}
+ zero padding: 3
diff --git a/parm/jcb-gdas/algorithm/snow/snow_addincrement.yaml.j2 b/parm/jcb-gdas/algorithm/snow/snow_addincrement.yaml.j2
new file mode 100644
index 000000000..1ac692e0d
--- /dev/null
+++ b/parm/jcb-gdas/algorithm/snow/snow_addincrement.yaml.j2
@@ -0,0 +1,43 @@
+state geometry:
+ fms initialization:
+ namelist filename: ./fv3jedi/fmsmpp.nml
+ field table filename: ./fv3jedi/field_table
+ akbk: ./fv3jedi/akbk.nc4
+ layout:
+ - {{ snow_layout_x }}
+ - {{ snow_layout_y }}
+ npx: {{ snow_npx_ges }}
+ npy: {{ snow_npy_ges }}
+ npz: {{ snow_npz_ges }}
+ field metadata override: ./fv3jedi/fv3jedi_fieldmetadata_history.yaml
+increment geometry:
+ fms initialization:
+ namelist filename: ./fv3jedi/fmsmpp.nml
+ field table filename: ./fv3jedi/field_table
+ akbk: ./fv3jedi/akbk.nc4
+ layout:
+ - {{ snow_layout_x }}
+ - {{ snow_layout_y }}
+ npx: {{ snow_npx_ges }}
+ npy: {{ snow_npy_ges }}
+ npz: {{ snow_npz_ges }}
+ field metadata override: ./fv3jedi/fv3jedi_fieldmetadata_restart.yaml
+state:
+ datetime: '{{ snow_background_time_iso }}'
+ state variables: {{ analysis_variables }}
+ filetype: cube sphere history
+ provider: ufs
+ datapath: ./
+ filename: {{ snow_variational_history_prefix }}cubed_sphere_grid_sfcf006.nc
+increment:
+ added variables: {{ analysis_variables }}
+ filetype: fms restart
+ datapath: ./
+ filename is datetime templated: true
+ filename_sfcd: '%yyyy%mm%dd.%hh%MM%ss.sfc_data.nc'
+ prefix: snowinc
+output:
+ filetype: auxgrid
+ gridtype: gaussian
+ datapath: ./
+ filename: snowanl.
diff --git a/parm/jcb-gdas/algorithm/snow/snow_ims_scf_preprocess.yaml.j2 b/parm/jcb-gdas/algorithm/snow/snow_ims_scf_preprocess.yaml.j2
new file mode 100644
index 000000000..7d5f4e9e0
--- /dev/null
+++ b/parm/jcb-gdas/algorithm/snow/snow_ims_scf_preprocess.yaml.j2
@@ -0,0 +1,42 @@
+geometry:
+ fms initialization:
+ namelist filename: ./fv3jedi/fmsmpp.nml
+ field table filename: ./fv3jedi/field_table
+ akbk: ./fv3jedi/akbk.nc4
+ layout:
+ - {{snow_layout_x}}
+ - {{snow_layout_y}}
+ npx: {{ snow_npx_ges }}
+ npy: {{ snow_npy_ges }}
+ npz: {{ snow_npz_ges }}
+ time invariant fields:
+ state fields:
+ datapath: {{ snow_background_path }}
+ filetype: fms restart
+ skip coupler file: true
+ datetime: '{{ snow_background_time_iso }}'
+ state variables:
+ - filtered_orography
+ field io names:
+ filtered_orography: orog_filt
+ filename_sfcd: '{{ snow_background_time_fv3 }}.sfc_data.nc'
+ filename_cplr: '{{ snow_background_time_fv3 }}.coupler.res'
+ filename_orog: '{{ snow_orog_prefix }}_oro_data.nc'
+date: '{{ snow_background_time_iso }}'
+output ioda file: '{{snow_obsdatain_path}}/{{snow_obsdatain_prefix}}ims_snow.tm00.nc'
+input scf file: './obs/ims{{ snow_background_time_julian }}_4km_v1.3.{{ ims_scf_obs_suffix }}'
+mapping file: './obs/IMS4km_to_FV3_mapping.{{ snow_orog_prefix }}_oro_data.nc'
+variables:
+- totalSnowDepth
+- vtype
+- slmsk
+- sheleg
+- filtered_orography
+- fraction_of_ice
+- fraction_of_land
+- stc
+background:
+{% filter indent(width=2) %}
+{% set background_file = background_file|default(model_component ~ 'background', true) ~ '.yaml.j2' %}
+{% include background_file %}
+{% endfilter %}
diff --git a/parm/jcb-gdas/algorithm/soil/soil_addincrement.yaml.j2 b/parm/jcb-gdas/algorithm/soil/soil_addincrement.yaml.j2
new file mode 100644
index 000000000..d6f01865f
--- /dev/null
+++ b/parm/jcb-gdas/algorithm/soil/soil_addincrement.yaml.j2
@@ -0,0 +1,74 @@
+state geometry:
+ fms initialization:
+ namelist filename: ./fv3jedi/fmsmpp.nml
+ field table filename: ./fv3jedi/field_table
+ akbk: ./fv3jedi/akbk.nc4
+ layout:
+ - {{ soil_layout_x }}
+ - {{ soil_layout_y }}
+ npx: {{ soil_npx_ges }}
+ npy: {{ soil_npy_ges }}
+ npz: {{ soil_npz_ges }}
+# field metadata override: ./fv3jedi/fv3jedi_fieldmetadata_history.yaml
+increment geometry:
+ fms initialization:
+ namelist filename: ./fv3jedi/fmsmpp.nml
+ field table filename: ./fv3jedi/field_table
+ akbk: ./fv3jedi/akbk.nc4
+ layout:
+ - {{ soil_layout_x }}
+ - {{ soil_layout_y }}
+ npx: {{ soil_npx_anl }}
+ npy: {{ soil_npy_anl }}
+ npz: {{ soil_npz_anl }}
+# field metadata override: ./fv3jedi/fv3jedi_fieldmetadata_fv3inc.yaml
+state:
+ state variables:
+ - soilMoistureVolumetric
+ - stc
+ - totalSnowDepth
+ - sheleg
+ - vtype
+ - slmsk
+ - fraction_of_ice
+ field io names:
+ totalSnowDepth: snodl
+ soilMoistureVolumetric: smc
+ fraction_of_ice: fice
+ datapath: ./bkg
+ filetype: fms restart
+ skip coupler file: true
+ datetime: '{{ soil_background_time_iso }}'
+ filename_sfcd: {{ soil_background_time_fv3 }}.sfc_data.nc
+increment:
+ added variables:
+ - soilMoistureVolumetric
+ field io names:
+ soilMoistureVolumetric: smc
+ datapath: ./anl
+ filetype: fms restart
+ skip coupler file: true
+ prefix: soilinc
+ filename is datetime templated: true
+ datetime: '{{ soil_background_time_iso }}'
+ filename_sfcd: {{ soil_background_time_fv3 }}.sfc_data.nc
+output:
+ datapath: ./anl
+ prefix: soilanl
+ filetype: fms restart
+ skip coupler file: true
+ filename is datetime templated: true
+ datetime: '{{ soil_background_time_iso }}'
+ filename_sfcd: {{ soil_background_time_fv3 }}.sfc_data.nc
+ state variables:
+ - soilMoistureVolumetric
+ - stc
+ - totalSnowDepth
+ - sheleg
+ - vtype
+ - slmsk
+ - fraction_of_ice
+ field io names:
+ soilMoistureVolumetric: smc
+ totalSnowDepth: snodl
+ fraction_of_ice: fice
diff --git a/parm/jcb-gdas/model/aero/aero_3dfgat_outer_loop_1.yaml.j2 b/parm/jcb-gdas/model/aero/aero_3dfgat_outer_loop_1.yaml.j2
new file mode 120000
index 000000000..be2ee77a8
--- /dev/null
+++ b/parm/jcb-gdas/model/aero/aero_3dfgat_outer_loop_1.yaml.j2
@@ -0,0 +1 @@
+aero_3dvar_outer_loop_1.yaml.j2
\ No newline at end of file
diff --git a/parm/jcb-gdas/model/aero/aero_3dfgat_outer_loop_2.yaml.j2 b/parm/jcb-gdas/model/aero/aero_3dfgat_outer_loop_2.yaml.j2
new file mode 120000
index 000000000..d029b98df
--- /dev/null
+++ b/parm/jcb-gdas/model/aero/aero_3dfgat_outer_loop_2.yaml.j2
@@ -0,0 +1 @@
+aero_3dvar_outer_loop_2.yaml.j2
\ No newline at end of file
diff --git a/parm/jcb-gdas/model/aero/aero_3dvar_outer_loop_1.yaml.j2 b/parm/jcb-gdas/model/aero/aero_3dvar_outer_loop_1.yaml.j2
new file mode 100644
index 000000000..2c6183651
--- /dev/null
+++ b/parm/jcb-gdas/model/aero/aero_3dvar_outer_loop_1.yaml.j2
@@ -0,0 +1,16 @@
+- ninner: 35
+ gradient norm reduction: 1e-10
+ test: on
+ 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_anl}}
+ npy: {{aero_npy_anl}}
+ npz: {{aero_npz_anl}}
+ diagnostics:
+ departures: bkgmob
diff --git a/parm/jcb-gdas/model/aero/aero_3dvar_outer_loop_2.yaml.j2 b/parm/jcb-gdas/model/aero/aero_3dvar_outer_loop_2.yaml.j2
new file mode 100644
index 000000000..edd109797
--- /dev/null
+++ b/parm/jcb-gdas/model/aero/aero_3dvar_outer_loop_2.yaml.j2
@@ -0,0 +1,16 @@
+- ninner: 35
+ gradient norm reduction: 1e-10
+ test: on
+ 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_anl}}
+ npy: {{aero_npy_anl}}
+ npz: {{aero_npz_anl}}
+ diagnostics:
+ departures: bkgmob1
diff --git a/parm/jcb-gdas/model/aero/aero_background.yaml.j2 b/parm/jcb-gdas/model/aero/aero_background.yaml.j2
new file mode 100644
index 000000000..daf6d4ef8
--- /dev/null
+++ b/parm/jcb-gdas/model/aero/aero_background.yaml.j2
@@ -0,0 +1,43 @@
+datapath: {{ aero_background_path }}
+filetype: fms restart
+datetime: '{{ aero_background_time_iso }}'
+filename is datetime templated: true
+filename_core: '%yyyy%mm%dd.%hh%MM%ss.fv_core.res.nc'
+filename_trcr: '%yyyy%mm%dd.%hh%MM%ss.fv_tracer.res.nc'
+filename_cplr: '%yyyy%mm%dd.%hh%MM%ss.coupler.res'
+state variables:
+- air_temperature
+- air_pressure_thickness
+- water_vapor_mixing_ratio_wrt_moist_air
+- mass_fraction_of_sulfate_in_air
+- mass_fraction_of_hydrophobic_black_carbon_in_air
+- mass_fraction_of_hydrophilic_black_carbon_in_air
+- mass_fraction_of_hydrophobic_organic_carbon_in_air
+- mass_fraction_of_hydrophilic_organic_carbon_in_air
+- mass_fraction_of_dust001_in_air
+- mass_fraction_of_dust002_in_air
+- mass_fraction_of_dust003_in_air
+- mass_fraction_of_dust004_in_air
+- mass_fraction_of_dust005_in_air
+- mass_fraction_of_sea_salt001_in_air
+- mass_fraction_of_sea_salt002_in_air
+- mass_fraction_of_sea_salt003_in_air
+- mass_fraction_of_sea_salt004_in_air
+field io names:
+ air_temperature: T
+ air_pressure_thickness: delp
+ water_vapor_mixing_ratio_wrt_moist_air: sphum
+ mass_fraction_of_sulfate_in_air: so4
+ mass_fraction_of_hydrophobic_black_carbon_in_air: bc1
+ mass_fraction_of_hydrophilic_black_carbon_in_air: bc2
+ mass_fraction_of_hydrophobic_organic_carbon_in_air: oc1
+ mass_fraction_of_hydrophilic_organic_carbon_in_air: oc2
+ mass_fraction_of_dust001_in_air: dust1
+ mass_fraction_of_dust002_in_air: dust2
+ mass_fraction_of_dust003_in_air: dust3
+ mass_fraction_of_dust004_in_air: dust4
+ mass_fraction_of_dust005_in_air: dust5
+ mass_fraction_of_sea_salt001_in_air: seas2
+ mass_fraction_of_sea_salt002_in_air: seas3
+ mass_fraction_of_sea_salt003_in_air: seas4
+ mass_fraction_of_sea_salt004_in_air: seas5
diff --git a/parm/jcb-gdas/model/aero/aero_background_error_static_diffusion.yaml.j2 b/parm/jcb-gdas/model/aero/aero_background_error_static_diffusion.yaml.j2
new file mode 100644
index 000000000..cb29115f3
--- /dev/null
+++ b/parm/jcb-gdas/model/aero/aero_background_error_static_diffusion.yaml.j2
@@ -0,0 +1,53 @@
+covariance model: SABER
+saber central block:
+ saber block name: diffusion
+ read:
+ groups:
+ - variables:
+ - mass_fraction_of_sulfate_in_air
+ - mass_fraction_of_hydrophobic_black_carbon_in_air
+ - mass_fraction_of_hydrophilic_black_carbon_in_air
+ - mass_fraction_of_hydrophobic_organic_carbon_in_air
+ - mass_fraction_of_hydrophilic_organic_carbon_in_air
+ - mass_fraction_of_dust001_in_air
+ - mass_fraction_of_dust002_in_air
+ - mass_fraction_of_dust003_in_air
+ - mass_fraction_of_dust004_in_air
+ - mass_fraction_of_dust005_in_air
+ - mass_fraction_of_sea_salt001_in_air
+ - mass_fraction_of_sea_salt002_in_air
+ - mass_fraction_of_sea_salt003_in_air
+ - mass_fraction_of_sea_salt004_in_air
+ horizontal:
+ filepath: "{{aero_berror_data_directory}}/diffusion_hz"
+ vertical:
+ levels: {{aero_npz_anl}}
+ filepath: "{{aero_berror_data_directory}}/diffusion_vt"
+saber outer blocks:
+- saber block name: StdDev
+ read:
+ model file:
+ datetime: "{{ aero_cycle_time_iso }}"
+ set datetime on read: true
+ filetype: fms restart
+ psinfile: true
+ datapath: "{{aero_berror_data_directory}}"
+ filename_core: '{{ aero_cycle_time_fv3 }}.stddev.fv_core.res.nc'
+ filename_trcr: '{{ aero_cycle_time_fv3 }}.stddev.fv_tracer.res.nc'
+ filename_cplr: '{{ aero_cycle_time_fv3 }}.stddev.coupler.res'
+ date: "{{ aero_cycle_time_iso }}"
+ field io names:
+ mass_fraction_of_dust001_in_air: dust1
+ mass_fraction_of_dust002_in_air: dust2
+ mass_fraction_of_dust003_in_air: dust3
+ mass_fraction_of_dust004_in_air: dust4
+ mass_fraction_of_dust005_in_air: dust5
+ mass_fraction_of_sea_salt001_in_air: seas2
+ mass_fraction_of_sea_salt002_in_air: seas3
+ mass_fraction_of_sea_salt003_in_air: seas4
+ mass_fraction_of_sea_salt004_in_air: seas5
+ mass_fraction_of_hydrophobic_black_carbon_in_air: bc1
+ mass_fraction_of_hydrophilic_black_carbon_in_air: bc2
+ mass_fraction_of_hydrophobic_organic_carbon_in_air: oc1
+ mass_fraction_of_hydrophilic_organic_carbon_in_air: oc2
+ mass_fraction_of_sulfate_in_air: so4
diff --git a/parm/jcb-gdas/model/aero/aero_final_increment_cubed_sphere.yaml.j2 b/parm/jcb-gdas/model/aero/aero_final_increment_cubed_sphere.yaml.j2
new file mode 100644
index 000000000..74c96986b
--- /dev/null
+++ b/parm/jcb-gdas/model/aero/aero_final_increment_cubed_sphere.yaml.j2
@@ -0,0 +1,55 @@
+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_ges}}
+ npy: {{aero_npy_ges}}
+ npz: {{aero_npz_ges}}
+output:
+ state component:
+ datapath: {{ aero_analysis_path }}
+ prefix: aeroinc
+ filetype: fms restart
+ filename_core: '{{ aero_cycle_time_fv3 }}.fv_core.res.nc'
+ filename_trcr: '{{ aero_cycle_time_fv3 }}.fv_tracer.res.nc'
+ filename_cplr: '{{ aero_cycle_time_fv3 }}.coupler.res'
+ state variables:
+ - air_temperature
+ - air_pressure_thickness
+ - water_vapor_mixing_ratio_wrt_moist_air
+ - mass_fraction_of_sulfate_in_air
+ - mass_fraction_of_hydrophobic_black_carbon_in_air
+ - mass_fraction_of_hydrophilic_black_carbon_in_air
+ - mass_fraction_of_hydrophobic_organic_carbon_in_air
+ - mass_fraction_of_hydrophilic_organic_carbon_in_air
+ - mass_fraction_of_dust001_in_air
+ - mass_fraction_of_dust002_in_air
+ - mass_fraction_of_dust003_in_air
+ - mass_fraction_of_dust004_in_air
+ - mass_fraction_of_dust005_in_air
+ - mass_fraction_of_sea_salt001_in_air
+ - mass_fraction_of_sea_salt002_in_air
+ - mass_fraction_of_sea_salt003_in_air
+ - mass_fraction_of_sea_salt004_in_air
+ field io names:
+ air_temperature: T
+ air_pressure_thickness: delp
+ water_vapor_mixing_ratio_wrt_moist_air: sphum
+ mass_fraction_of_dust001_in_air: dust1
+ mass_fraction_of_dust002_in_air: dust2
+ mass_fraction_of_dust003_in_air: dust3
+ mass_fraction_of_dust004_in_air: dust4
+ mass_fraction_of_dust005_in_air: dust5
+ mass_fraction_of_sea_salt001_in_air: seas2
+ mass_fraction_of_sea_salt002_in_air: seas3
+ mass_fraction_of_sea_salt003_in_air: seas4
+ mass_fraction_of_sea_salt004_in_air: seas5
+ mass_fraction_of_hydrophobic_black_carbon_in_air: bc1
+ mass_fraction_of_hydrophilic_black_carbon_in_air: bc2
+ mass_fraction_of_hydrophobic_organic_carbon_in_air: oc1
+ mass_fraction_of_hydrophilic_organic_carbon_in_air: oc2
+ mass_fraction_of_sulfate_in_air: so4
diff --git a/parm/jcb-gdas/model/aero/aero_final_increment_gaussian.yaml.j2 b/parm/jcb-gdas/model/aero/aero_final_increment_gaussian.yaml.j2
new file mode 100644
index 000000000..87f0b689f
--- /dev/null
+++ b/parm/jcb-gdas/model/aero/aero_final_increment_gaussian.yaml.j2
@@ -0,0 +1,23 @@
+grid type: regular gaussian
+local interpolator type: atlas interpolator
+interpolation method:
+ type: finite-element
+number of latitude gridpoints: {{ aero_npy_anl - 1 }}
+variables to output:
+- mass_fraction_of_sulfate_in_air
+- mass_fraction_of_hydrophobic_black_carbon_in_air
+- mass_fraction_of_hydrophilic_black_carbon_in_air
+- mass_fraction_of_hydrophobic_organic_carbon_in_air
+- mass_fraction_of_hydrophilic_organic_carbon_in_air
+- mass_fraction_of_dust001_in_air
+- mass_fraction_of_dust002_in_air
+- mass_fraction_of_dust003_in_air
+- mass_fraction_of_dust004_in_air
+- mass_fraction_of_dust005_in_air
+- mass_fraction_of_sea_salt001_in_air
+- mass_fraction_of_sea_salt002_in_air
+- mass_fraction_of_sea_salt003_in_air
+- mass_fraction_of_sea_salt004_in_air
+all model levels: true
+datapath: {{ aero_analysis_path }}
+prefix: aeroinc_gauss
diff --git a/parm/jcb-gdas/model/aero/aero_geometry_background.yaml.j2 b/parm/jcb-gdas/model/aero/aero_geometry_background.yaml.j2
new file mode 100644
index 000000000..b55f395ab
--- /dev/null
+++ b/parm/jcb-gdas/model/aero/aero_geometry_background.yaml.j2
@@ -0,0 +1,10 @@
+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_ges}}
+npy: {{aero_npy_ges}}
+npz: {{aero_npz_ges}}
diff --git a/parm/jcb-gdas/model/aero/aero_model_pseudo.yaml.j2 b/parm/jcb-gdas/model/aero/aero_model_pseudo.yaml.j2
new file mode 100644
index 000000000..a5c879a5b
--- /dev/null
+++ b/parm/jcb-gdas/model/aero/aero_model_pseudo.yaml.j2
@@ -0,0 +1,46 @@
+name: PSEUDO
+datapath: {{ aero_background_path}}
+filetype: fms restart
+filename is datetime templated: true
+filename_core: '%yyyy%mm%dd.%hh%MM%ss.fv_core.res.nc'
+filename_trcr: '%yyyy%mm%dd.%hh%MM%ss.fv_tracer.res.nc'
+filename_sfcd: '%yyyy%mm%dd.%hh%MM%ss.sfc_data.nc'
+filename_sfcw: '%yyyy%mm%dd.%hh%MM%ss.fv_srf_wnd.res.nc'
+filename_cplr: '%yyyy%mm%dd.%hh%MM%ss.coupler.res'
+state variables:
+- air_temperature
+- air_pressure_thickness
+- water_vapor_mixing_ratio_wrt_moist_air
+- mass_fraction_of_sulfate_in_air
+- mass_fraction_of_hydrophobic_black_carbon_in_air
+- mass_fraction_of_hydrophilic_black_carbon_in_air
+- mass_fraction_of_hydrophobic_organic_carbon_in_air
+- mass_fraction_of_hydrophilic_organic_carbon_in_air
+- mass_fraction_of_dust001_in_air
+- mass_fraction_of_dust002_in_air
+- mass_fraction_of_dust003_in_air
+- mass_fraction_of_dust004_in_air
+- mass_fraction_of_dust005_in_air
+- mass_fraction_of_sea_salt001_in_air
+- mass_fraction_of_sea_salt002_in_air
+- mass_fraction_of_sea_salt003_in_air
+- mass_fraction_of_sea_salt004_in_air
+field io names:
+ air_temperature: T
+ air_pressure_thickness: delp
+ water_vapor_mixing_ratio_wrt_moist_air: sphum
+ mass_fraction_of_sulfate_in_air: so4
+ mass_fraction_of_hydrophobic_black_carbon_in_air: bc1
+ mass_fraction_of_hydrophilic_black_carbon_in_air: bc2
+ mass_fraction_of_hydrophobic_organic_carbon_in_air: oc1
+ mass_fraction_of_hydrophilic_organic_carbon_in_air: oc2
+ mass_fraction_of_dust001_in_air: dust1
+ mass_fraction_of_dust002_in_air: dust2
+ mass_fraction_of_dust003_in_air: dust3
+ mass_fraction_of_dust004_in_air: dust4
+ mass_fraction_of_dust005_in_air: dust5
+ mass_fraction_of_sea_salt001_in_air: seas2
+ mass_fraction_of_sea_salt002_in_air: seas3
+ mass_fraction_of_sea_salt003_in_air: seas4
+ mass_fraction_of_sea_salt004_in_air: seas5
+tstep: {{aero_forecast_timestep}}
diff --git a/parm/jcb-gdas/model/atmosphere/atmosphere_3dvar_outer_loop_1.yaml.j2 b/parm/jcb-gdas/model/atmosphere/atmosphere_3dvar_outer_loop_1.yaml.j2
new file mode 100644
index 000000000..bcb4a4600
--- /dev/null
+++ b/parm/jcb-gdas/model/atmosphere/atmosphere_3dvar_outer_loop_1.yaml.j2
@@ -0,0 +1,17 @@
+- ninner: {{atmosphere_ninner_1}}
+ gradient norm reduction: {{atmosphere_grad_red_1}}
+ test: on
+ geometry:
+ fms initialization:
+ namelist filename: {{atmosphere_fv3jedi_files_path}}/fmsmpp.nml
+ field table filename: {{atmosphere_fv3jedi_files_path}}/field_table
+ akbk: {{atmosphere_fv3jedi_files_path}}/akbk.nc4
+ layout:
+ - {{atmosphere_layout_x}}
+ - {{atmosphere_layout_y}}
+ npx: {{atmosphere_npx_anl}}
+ npy: {{atmosphere_npy_anl}}
+ npz: {{atmosphere_npz_anl}}
+ vert coordinate: logp
+ diagnostics:
+ departures: bkgmob
diff --git a/parm/jcb-gdas/model/atmosphere/atmosphere_3dvar_outer_loop_2.yaml.j2 b/parm/jcb-gdas/model/atmosphere/atmosphere_3dvar_outer_loop_2.yaml.j2
new file mode 100644
index 000000000..ab5b15d22
--- /dev/null
+++ b/parm/jcb-gdas/model/atmosphere/atmosphere_3dvar_outer_loop_2.yaml.j2
@@ -0,0 +1,17 @@
+- ninner: {{atmosphere_ninner_2}}
+ gradient norm reduction: {{atmosphere_grad_red_2}}
+ test: on
+ geometry:
+ fms initialization:
+ namelist filename: {{atmosphere_fv3jedi_files_path}}/fmsmpp.nml
+ field table filename: {{atmosphere_fv3jedi_files_path}}/field_table
+ akbk: {{atmosphere_fv3jedi_files_path}}/akbk.nc4
+ layout:
+ - {{atmosphere_layout_x}}
+ - {{atmosphere_layout_y}}
+ npx: {{atmosphere_npx_anl}}
+ npy: {{atmosphere_npy_anl}}
+ npz: {{atmosphere_npz_anl}}
+ vert coordinate: logp
+ diagnostics:
+ departures: bkgmob1
diff --git a/parm/jcb-gdas/model/atmosphere/atmosphere_background.yaml.j2 b/parm/jcb-gdas/model/atmosphere/atmosphere_background.yaml.j2
new file mode 100644
index 000000000..f5a10238a
--- /dev/null
+++ b/parm/jcb-gdas/model/atmosphere/atmosphere_background.yaml.j2
@@ -0,0 +1,63 @@
+datapath: {{ atmosphere_background_path }}
+filetype: cube sphere history
+provider: ufs
+datetime: "{{ atmosphere_background_time_iso }}"
+filenames:
+- {{ atmosphere_variational_history_prefix }}cubed_sphere_grid_atmf006.nc
+- {{ atmosphere_variational_history_prefix }}cubed_sphere_grid_sfcf006.nc
+max allowable geometry difference: 1e-4
+state variables:
+- eastward_wind
+- northward_wind
+- air_temperature
+- air_pressure_thickness
+- air_pressure_at_surface
+- water_vapor_mixing_ratio_wrt_moist_air
+- cloud_liquid_ice
+- cloud_liquid_water
+- snow_water
+- rain_water
+- graupel
+- cloud_ice_number_concentration
+- rain_number_concentration
+- ozone_mass_mixing_ratio
+- geopotential_height_at_surface
+- slmsk
+- sheleg
+- skin_temperature_at_surface
+- vtype
+- stype
+- vfrac
+- soilt
+- soilm
+- totalSnowDepthMeters
+- eastward_wind_at_surface
+- northward_wind_at_surface
+- f10m
+field io names:
+ eastward_wind: ugrd
+ northward_wind: vgrd
+ air_temperature: tmp
+ layer_thickness: delz
+ air_pressure_thickness: dpres
+ air_pressure_at_surface: pressfc
+ water_vapor_mixing_ratio_wrt_moist_air: spfh
+ cloud_liquid_ice: icmr
+ cloud_liquid_water: clwmr
+ snow_water: snmr
+ rain_water: rwmr
+ graupel: grle
+ cloud_ice_number_concentration: nccice
+ rain_number_concentration: nconrd
+ ozone_mass_mixing_ratio: o3mr
+ geopotential_height_at_surface: hgtsfc
+ slmsk: land
+ sheleg: weasd
+ skin_temperature_at_surface: tmpsfc
+ stype: sotyp
+ vfrac: veg
+ totalSnowDepthMeters: snod
+ eastward_wind_at_surface: ugrd_hyblev1
+ northward_wind_at_surface: vgrd_hyblev1
+ soilm: soilw1
+ soilt: soilt1
diff --git a/parm/jcb-gdas/model/atmosphere/atmosphere_background_ensemble.yaml.j2 b/parm/jcb-gdas/model/atmosphere/atmosphere_background_ensemble.yaml.j2
new file mode 100644
index 000000000..a9e96487c
--- /dev/null
+++ b/parm/jcb-gdas/model/atmosphere/atmosphere_background_ensemble.yaml.j2
@@ -0,0 +1,71 @@
+datetime: '{{ atmosphere_background_time_iso }}'
+members from template:
+ template:
+ datetime: '{{ atmosphere_background_time_iso }}'
+ filetype: cube sphere history
+ provider: ufs
+ state variables:
+ - eastward_wind
+ - northward_wind
+ - air_temperature
+ - layer_thickness
+ - air_pressure_thickness
+ - air_pressure_at_surface
+ - water_vapor_mixing_ratio_wrt_moist_air
+ - cloud_liquid_ice
+ - cloud_liquid_water
+ - snow_water
+ - rain_water
+ - graupel
+ - cloud_ice_number_concentration
+ - rain_number_concentration
+ - ozone_mass_mixing_ratio
+ - geopotential_height_at_surface
+ - slmsk
+ - sheleg
+ - skin_temperature_at_surface
+ - vtype
+ - stype
+ - vfrac
+ - soilt
+ - soilm
+ - totalSnowDepthMeters
+ - eastward_wind_at_surface
+ - northward_wind_at_surface
+ - f10m
+ field io names:
+ eastward_wind: ugrd
+ northward_wind: vgrd
+ air_temperature: tmp
+ layer_thickness: delz
+ air_pressure_thickness: dpres
+ air_pressure_at_surface: pressfc
+ water_vapor_mixing_ratio_wrt_moist_air: spfh
+ cloud_liquid_ice: icmr
+ cloud_liquid_water: clwmr
+ snow_water: snmr
+ rain_water: rwmr
+ graupel: grle
+ cloud_ice_number_concentration: nccice
+ rain_number_concentration: nconrd
+ ozone_mass_mixing_ratio: o3mr
+ geopotential_height_at_surface: hgtsfc
+ slmsk: land
+ sheleg: weasd
+ skin_temperature_at_surface: tmpsfc
+ stype: sotyp
+ vfrac: veg
+ totalSnowDepthMeters: snod
+ eastward_wind_at_surface: ugrd_hyblev1
+ northward_wind_at_surface: vgrd_hyblev1
+ soilm: soilw1
+ soilt: soilt1
+ datapath: {{ atmosphere_background_ensemble_path }}
+ filename is datetime templated: true
+ filenames:
+ - {{ atmosphere_ensemble_history_prefix }}cubed_sphere_grid_atmf006.nc
+ - {{ atmosphere_ensemble_history_prefix }}cubed_sphere_grid_sfcf006.nc
+ max allowable geometry difference: 1e-4
+ pattern: "{{ atmosphere_ensemble_pattern | default("%mem%", true) }}"
+ nmembers: {{ atmosphere_number_ensemble_members }}
+ zero padding: 3
diff --git a/parm/jcb-gdas/model/atmosphere/atmosphere_background_error_hybrid_gsibec_bump.yaml.j2 b/parm/jcb-gdas/model/atmosphere/atmosphere_background_error_hybrid_gsibec_bump.yaml.j2
new file mode 100644
index 000000000..316dc6d6e
--- /dev/null
+++ b/parm/jcb-gdas/model/atmosphere/atmosphere_background_error_hybrid_gsibec_bump.yaml.j2
@@ -0,0 +1,290 @@
+covariance model: hybrid
+components:
+- covariance:
+ covariance model: SABER
+ saber central block:
+ saber block name: gsi static covariance
+ read:
+ gsi akbk: {{atmosphere_fv3jedi_files_path}}/akbk.nc4
+ gsi error covariance file: {{atmosphere_gsibec_path}}/gsi-coeffs-gfs-global.nc4
+ gsi berror namelist file: {{atmosphere_gsibec_path}}/gfs_gsi_global.nml
+ processor layout x direction: {{atmosphere_layout_gsib_x}}
+ processor layout y direction: {{atmosphere_layout_gsib_y}}
+ debugging mode: false
+ saber outer blocks:
+ - saber block name: interpolation
+ inner geometry:
+ function space: StructuredColumns
+ custom grid matching gsi:
+ type: gaussian
+ lats: {{ atmosphere_npy_ges + 1 }}
+ {% set atmosphere_lons = (atmosphere_npx_ges - 1) * 2 %}
+ lons: {{ atmosphere_lons }}
+ custom partitioner matching gsi:
+ bands: {{ atmosphere_layout_gsib_y }}
+ halo: 1
+ forward interpolator:
+ local interpolator type: oops unstructured grid interpolator
+ inverse interpolator:
+ local interpolator type: oops unstructured grid interpolator
+ state variables to inverse: [eastward_wind,northward_wind,air_temperature,air_pressure_at_surface,
+ water_vapor_mixing_ratio_wrt_moist_air,cloud_liquid_ice,cloud_liquid_water,
+ snow_water,rain_water,graupel,ozone_mass_mixing_ratio]
+ linear variable change:
+ linear variable change name: Control2Analysis
+ input variables:
+ - eastward_wind
+ - northward_wind
+ - air_temperature
+ - air_pressure_at_surface
+ - water_vapor_mixing_ratio_wrt_moist_air
+ - cloud_liquid_ice
+ - cloud_liquid_water
+ - snow_water
+ - rain_water
+ - graupel
+ - mole_fraction_of_ozone_in_air
+ output variables:
+ - eastward_wind
+ - northward_wind
+ - air_temperature
+ - air_pressure_at_surface
+ - water_vapor_mixing_ratio_wrt_moist_air
+ - cloud_liquid_ice
+ - cloud_liquid_water
+ - snow_water
+ - rain_water
+ - graupel
+ - ozone_mass_mixing_ratio
+ weight:
+ value: 0.125
+- covariance:
+ covariance model: ensemble
+ members from template:
+ template:
+ datetime: "{{ atmosphere_background_time_iso }}"
+ filetype: cube sphere history
+ provider: ufs
+ state variables:
+ - eastward_wind
+ - northward_wind
+ - air_temperature
+ - air_pressure_at_surface
+ - water_vapor_mixing_ratio_wrt_moist_air
+ - cloud_liquid_ice
+ - cloud_liquid_water
+ - snow_water
+ - rain_water
+ - graupel
+ - ozone_mass_mixing_ratio
+ field io names:
+ eastward_wind: ugrd
+ northward_wind: vgrd
+ air_temperature: tmp
+ air_pressure_at_surface: pressfc
+ water_vapor_mixing_ratio_wrt_moist_air: spfh
+ cloud_liquid_ice: icmr
+ cloud_liquid_water: clwmr
+ snow_water: snmr
+ rain_water: rwmr
+ graupel: grle
+ ozone_mass_mixing_ratio: o3mr
+ datapath: {{ atmosphere_background_ensemble_path }}
+ filename is datetime templated: true
+ filenames:
+ - {{ atmosphere_ensemble_history_prefix }}cubed_sphere_grid_atmf006.nc
+ - {{ atmosphere_ensemble_history_prefix }}cubed_sphere_grid_sfcf006.nc
+ max allowable geometry difference: 1e-4
+ pattern: "{{ atmosphere_ensemble_pattern | default("%mem%", true) }}"
+ nmembers: {{atmosphere_number_ensemble_members}}
+ zero padding: 3
+ localization:
+ localization method: SABER
+ saber central block:
+ saber block name: BUMP_NICAS
+ active variables:
+ - eastward_wind
+ - northward_wind
+ - air_temperature
+ - air_pressure_at_surface
+ - water_vapor_mixing_ratio_wrt_moist_air
+ - cloud_liquid_ice
+ - cloud_liquid_water
+ - snow_water
+ - rain_water
+ - graupel
+ - ozone_mass_mixing_ratio
+ read:
+ general:
+ universe length-scale: 4641.0e3
+ drivers:
+ multivariate strategy: duplicated
+ compute nicas: true
+ model:
+ level for 2d variables: last
+ nicas:
+ resolution: 6
+ explicit length-scales: true
+ horizontal length-scale:
+ - groups:
+ - common
+ profile:
+ - 4641000.0
+ - 4641000.0
+ - 4641000.0
+ - 4641000.0
+ - 4641000.0
+ - 4641000.0
+ - 4641000.0
+ - 4641000.0
+ - 4641000.0
+ - 4641000.0
+ - 4641000.0
+ - 4462500.0
+ - 4462500.0
+ - 4284000.0
+ - 4284000.0
+ - 4105500.0
+ - 4105500.0
+ - 3927000.0
+ - 3927000.0
+ - 3570000.0
+ - 3570000.0
+ - 3570000.0
+ - 3570000.0
+ - 3570000.0
+ - 3570000.0
+ - 3570000.0
+ - 3570000.0
+ - 3570000.0
+ - 3570000.0
+ - 3570000.0
+ - 3570000.0
+ - 3570000.0
+ - 3570000.0
+ - 3570000.0
+ - 3570000.0
+ - 3570000.0
+ - 3570000.0
+ - 3570000.0
+ - 3570000.0
+ - 3391500.0
+ - 3391500.0
+ - 3213000.0
+ - 3213000.0
+ - 3034500.0
+ - 3034500.0
+ - 2856000.0
+ - 2856000.0
+ - 2677500.0
+ - 2677500.0
+ - 2374050.0
+ - 2374050.0
+ - 2088450.0
+ - 2088450.0
+ - 1820700.0
+ - 1820700.0
+ - 1570800.0
+ - 1570800.0
+ - 1392300.0
+ - 1392300.0
+ - 1356600.0
+ - 1356600.0
+ - 1320900.0
+ - 1320900.0
+ - 1285200.0
+ - 1285200.0
+ - 1249500.0
+ - 1249500.0
+ - 1249500.0
+ - 1249500.0
+ - 1249500.0
+ - 1249500.0
+ - 1249500.0
+ - 1249500.0
+ - 1249500.0
+ - 1249500.0
+ - 1249500.0
+ - 1249500.0
+ - 1249500.0
+ - 1249500.0
+ - 1249500.0
+ - 1249500.0
+ - 1249500.0
+ - 1249500.0
+ - 1249500.0
+ - 1249500.0
+ - 1249500.0
+ - 1249500.0
+ - 1249500.0
+ - 1249500.0
+ - 1249500.0
+ - 1249500.0
+ - 1249500.0
+ - 1249500.0
+ - 1249500.0
+ - 1249500.0
+ - 1249500.0
+ - 1249500.0
+ - 1249500.0
+ - 1249500.0
+ - 1249500.0
+ - 1249500.0
+ - 1249500.0
+ - 1249500.0
+ - 1249500.0
+ - 1249500.0
+ - 1249500.0
+ - 1249500.0
+ - 1249500.0
+ - 1249500.0
+ - 1249500.0
+ - 1249500.0
+ - 1249500.0
+ - 1249500.0
+ - 1249500.0
+ - 1249500.0
+ - 1249500.0
+ - 1249500.0
+ - 1249500.0
+ - 1249500.0
+ - 1249500.0
+ - 1249500.0
+ - 1249500.0
+ - 1249500.0
+ - 1249500.0
+ - 1249500.0
+ - 1249500.0
+ - 1249500.0
+ vertical length-scale:
+ - groups:
+ - common
+ value: 1.8
+ linear variable change:
+ linear variable change name: Control2Analysis
+ input variables:
+ - eastward_wind
+ - northward_wind
+ - air_temperature
+ - air_pressure_at_surface
+ - water_vapor_mixing_ratio_wrt_moist_air
+ - cloud_liquid_ice
+ - cloud_liquid_water
+ - snow_water
+ - rain_water
+ - graupel
+ - ozone_mass_mixing_ratio
+ output variables:
+ - eastward_wind
+ - northward_wind
+ - air_temperature
+ - air_pressure_at_surface
+ - water_vapor_mixing_ratio_wrt_moist_air
+ - cloud_liquid_ice
+ - cloud_liquid_water
+ - snow_water
+ - rain_water
+ - graupel
+ - ozone_mass_mixing_ratio
+ weight:
+ value: 0.875
diff --git a/parm/jcb-gdas/model/atmosphere/atmosphere_background_error_static_gsibec.yaml.j2 b/parm/jcb-gdas/model/atmosphere/atmosphere_background_error_static_gsibec.yaml.j2
new file mode 100644
index 000000000..2b6aa1700
--- /dev/null
+++ b/parm/jcb-gdas/model/atmosphere/atmosphere_background_error_static_gsibec.yaml.j2
@@ -0,0 +1,50 @@
+covariance model: SABER
+full inverse: true
+saber central block:
+ saber block name: gsi static covariance
+ read:
+ gsi akbk: {{atmosphere_fv3jedi_files_path}}/akbk.nc4
+ gsi error covariance file: {{atmosphere_gsibec_path}}/gsi-coeffs-gfs-global.nc4
+ gsi berror namelist file: {{atmosphere_gsibec_path}}/gfs_gsi_global.nml
+ processor layout x direction: {{atmosphere_layout_gsib_x}}
+ processor layout y direction: {{atmosphere_layout_gsib_y}}
+ debugging mode: false
+saber outer blocks:
+- saber block name: interpolation
+ inner geometry:
+ function space: StructuredColumns
+ custom grid matching gsi:
+ type: gaussian
+ lats: {{ atmosphere_npy_ges + 1 }}
+ {% set atmosphere_lons = (atmosphere_npx_ges - 1) * 2 %}
+ lons: {{ atmosphere_lons }}
+ custom partitioner matching gsi:
+ bands: {{ atmosphere_layout_gsib_y }}
+ halo: 1
+ forward interpolator:
+ local interpolator type: oops unstructured grid interpolator
+ inverse interpolator:
+ local interpolator type: oops unstructured grid interpolator
+ state variables to inverse: [eastward_wind,northward_wind,air_temperature,air_pressure_at_surface,
+ water_vapor_mixing_ratio_wrt_moist_air,cloud_liquid_ice,cloud_liquid_water,
+ ozone_mass_mixing_ratio]
+linear variable change:
+ linear variable change name: Control2Analysis
+ input variables:
+ - eastward_wind
+ - northward_wind
+ - air_temperature
+ - air_pressure_at_surface
+ - water_vapor_mixing_ratio_wrt_moist_air
+ - cloud_liquid_ice
+ - cloud_liquid_water
+ - mole_fraction_of_ozone_in_air
+ output variables:
+ - eastward_wind
+ - northward_wind
+ - air_temperature
+ - air_pressure_at_surface
+ - water_vapor_mixing_ratio_wrt_moist_air
+ - cloud_liquid_ice
+ - cloud_liquid_water
+ - ozone_mass_mixing_ratio
diff --git a/parm/jcb-gdas/model/atmosphere/atmosphere_background_error_static_identity.yaml.j2 b/parm/jcb-gdas/model/atmosphere/atmosphere_background_error_static_identity.yaml.j2
new file mode 100644
index 000000000..a2533ec23
--- /dev/null
+++ b/parm/jcb-gdas/model/atmosphere/atmosphere_background_error_static_identity.yaml.j2
@@ -0,0 +1,2 @@
+covariance model: FV3JEDI-ID
+date: "{{ atmosphere_background_time_iso }}"
diff --git a/parm/jcb-gdas/model/atmosphere/atmosphere_final_increment_cubed_sphere.yaml.j2 b/parm/jcb-gdas/model/atmosphere/atmosphere_final_increment_cubed_sphere.yaml.j2
new file mode 100644
index 000000000..a3af136c4
--- /dev/null
+++ b/parm/jcb-gdas/model/atmosphere/atmosphere_final_increment_cubed_sphere.yaml.j2
@@ -0,0 +1,40 @@
+output:
+ state component:
+ filetype: cube sphere history
+ filename: ./anl/cubed_sphere_grid_atminc.jedi.nc
+ provider: ufs
+ fields to write:
+ - eastward_wind
+ - northward_wind
+ - air_temperature
+ - air_pressure_at_surface
+ - water_vapor_mixing_ratio_wrt_moist_air
+ - cloud_liquid_ice
+ - cloud_liquid_water
+ - snow_water
+ - rain_water
+ - graupel
+ - ozone_mass_mixing_ratio
+ field io names:
+ eastward_wind: ugrd
+ northward_wind: vgrd
+ air_temperature: tmp
+ air_pressure_at_surface: pressfc
+ water_vapor_mixing_ratio_wrt_moist_air: spfh
+ cloud_liquid_ice: icmr
+ cloud_liquid_water: clwmr
+ snow_water: snmr
+ rain_water: rwmr
+ graupel: grle
+ ozone_mass_mixing_ratio: o3mr
+geometry:
+ fms initialization:
+ namelist filename: "{{atmosphere_fv3jedi_files_path}}/fmsmpp.nml"
+ field table filename: "{{atmosphere_fv3jedi_files_path}}/field_table"
+ akbk: "{{atmosphere_fv3jedi_files_path}}/akbk.nc4"
+ layout:
+ - {{atmosphere_layout_x}}
+ - {{atmosphere_layout_y}}
+ npx: {{atmosphere_npx_his}}
+ npy: {{atmosphere_npy_his}}
+ npz: {{atmosphere_npz_his}}
diff --git a/parm/jcb-gdas/model/atmosphere/atmosphere_final_increment_fms_nonrestart.yaml.j2 b/parm/jcb-gdas/model/atmosphere/atmosphere_final_increment_fms_nonrestart.yaml.j2
new file mode 100644
index 000000000..efac27abe
--- /dev/null
+++ b/parm/jcb-gdas/model/atmosphere/atmosphere_final_increment_fms_nonrestart.yaml.j2
@@ -0,0 +1,18 @@
+output:
+ state component:
+ filetype: fms restart
+ is restart: false
+ filename_nonrestart: ./anl/cubed_sphere_grid_atminc.jedi.nc
+ fields to write: [ua,va,t,ps,sphum,ice_wat,liq_wat,o3mr]
+geometry:
+ fms initialization:
+ namelist filename: "{{atmosphere_fv3jedi_files_path}}/fmsmpp.nml"
+ field table filename: "{{atmosphere_fv3jedi_files_path}}/field_table"
+ akbk: "{{atmosphere_fv3jedi_files_path}}/akbk.nc4"
+ layout:
+ - {{atmosphere_layout_x}}
+ - {{atmosphere_layout_y}}
+ npx: {{atmosphere_npx_ges}}
+ npy: {{atmosphere_npy_ges}}
+ npz: {{atmosphere_npz_ges}}
+ field metadata override: "{{atmosphere_fv3jedi_files_path}}/fv3jedi_fieldmetadata_fv3inc.yaml"
diff --git a/parm/jcb-gdas/model/atmosphere/atmosphere_final_increment_gaussian.yaml.j2 b/parm/jcb-gdas/model/atmosphere/atmosphere_final_increment_gaussian.yaml.j2
new file mode 100644
index 000000000..ae88b090f
--- /dev/null
+++ b/parm/jcb-gdas/model/atmosphere/atmosphere_final_increment_gaussian.yaml.j2
@@ -0,0 +1,25 @@
+output:
+ state component:
+ filetype: auxgrid
+ gridtype: gaussian
+ filename: {{atmosphere_final_increment_prefix}}
+ field io names:
+ eastward_wind: ugrd
+ northward_wind: vgrd
+ air_temperature: tmp
+ air_pressure_at_surface: pressfc
+ water_vapor_mixing_ratio_wrt_moist_air: spfh
+ cloud_liquid_ice: icmr
+ cloud_liquid_water: clwmr
+ ozone_mass_mixing_ratio: o3mr
+geometry:
+ fms initialization:
+ namelist filename: "{{atmosphere_fv3jedi_files_path}}/fmsmpp.nml"
+ field table filename: "{{atmosphere_fv3jedi_files_path}}/field_table"
+ akbk: "{{atmosphere_fv3jedi_files_path}}/akbk.nc4"
+ layout:
+ - {{atmosphere_layout_x}}
+ - {{atmosphere_layout_y}}
+ npx: {{atmosphere_npx_his}}
+ npy: {{atmosphere_npy_his}}
+ npz: {{atmosphere_npz_his}}
diff --git a/parm/jcb-gdas/model/atmosphere/atmosphere_geometry_background.yaml.j2 b/parm/jcb-gdas/model/atmosphere/atmosphere_geometry_background.yaml.j2
new file mode 100644
index 000000000..54e847648
--- /dev/null
+++ b/parm/jcb-gdas/model/atmosphere/atmosphere_geometry_background.yaml.j2
@@ -0,0 +1,10 @@
+fms initialization:
+ namelist filename: "{{atmosphere_fv3jedi_files_path}}/fmsmpp.nml"
+ field table filename: "{{atmosphere_fv3jedi_files_path}}/field_table"
+akbk: "{{atmosphere_fv3jedi_files_path}}/akbk.nc4"
+layout:
+- {{atmosphere_layout_x}}
+- {{atmosphere_layout_y}}
+npx: {{atmosphere_npx_ges}}
+npy: {{atmosphere_npy_ges}}
+npz: {{atmosphere_npz_ges}}
diff --git a/parm/jcb-gdas/model/atmosphere/atmosphere_model_pseudo.yaml.j2 b/parm/jcb-gdas/model/atmosphere/atmosphere_model_pseudo.yaml.j2
new file mode 100644
index 000000000..74af652ba
--- /dev/null
+++ b/parm/jcb-gdas/model/atmosphere/atmosphere_model_pseudo.yaml.j2
@@ -0,0 +1,32 @@
+name: PSEUDO
+datapath: {{ atmosphere_background_path}}
+filetype: fms restart
+filename is datetime templated: true
+filename_core: '%yyyy%mm%dd.%hh%MM%ss.fv_core.res.nc'
+filename_trcr: '%yyyy%mm%dd.%hh%MM%ss.fv_tracer.res.nc'
+filename_sfcd: '%yyyy%mm%dd.%hh%MM%ss.sfc_data.nc'
+filename_sfcw: '%yyyy%mm%dd.%hh%MM%ss.fv_srf_wnd.res.nc'
+filename_cplr: '%yyyy%mm%dd.%hh%MM%ss.coupler.res'
+tstep: {{atmosphere_forecast_timestep}}
+field io names:
+ eastward_wind: ugrd
+ northward_wind: vgrd
+ air_temperature: tmp
+ layer_thickness: delz
+ air_pressure_thickness: dpres
+ air_pressure_at_surface: pressfc
+ water_vapor_mixing_ratio_wrt_moist_air: spfh
+ cloud_liquid_ice: icmr
+ cloud_liquid_water: clwmr
+ ozone_mass_mixing_ratio: o3mr
+ geopotential_height_at_surface: hgtsfc
+ slmsk: land
+ sheleg: weasd
+ skin_temperature_at_surface: tmpsfc
+ stype: sotyp
+ vfrac: veg
+ totalSnowDepthMeters: snod
+ eastward_wind_at_surface: ugrd_hyblev1
+ northward_wind_at_surface: vgrd_hyblev1
+ soilm: soilw1
+ soilt: soilt1
diff --git a/parm/jcb-gdas/model/atmosphere/atmosphere_output_ensemble_increments_cubed_sphere.yaml.j2 b/parm/jcb-gdas/model/atmosphere/atmosphere_output_ensemble_increments_cubed_sphere.yaml.j2
new file mode 100644
index 000000000..7f159e380
--- /dev/null
+++ b/parm/jcb-gdas/model/atmosphere/atmosphere_output_ensemble_increments_cubed_sphere.yaml.j2
@@ -0,0 +1,15 @@
+filetype: cube sphere history
+provider: ufs
+filename: ./anl/mem%{member}%/cubed_sphere_grid_atminc.jedi.nc
+field io names:
+ eastward_wind: ugrd
+ northward_wind: vgrd
+ air_temperature: tmp
+ air_pressure_at_surface: pressfc
+ water_vapor_mixing_ratio_wrt_moist_air: spfh
+ cloud_liquid_ice: icmr
+ cloud_liquid_water: clwmr
+ snow_water: snmr
+ rain_water: rwmr
+ graupel: grle
+ ozone_mass_mixing_ratio: o3mr
diff --git a/parm/jcb-gdas/model/atmosphere/atmosphere_output_ensemble_increments_fms_nonrestart.yaml.j2 b/parm/jcb-gdas/model/atmosphere/atmosphere_output_ensemble_increments_fms_nonrestart.yaml.j2
new file mode 100644
index 000000000..ff021176f
--- /dev/null
+++ b/parm/jcb-gdas/model/atmosphere/atmosphere_output_ensemble_increments_fms_nonrestart.yaml.j2
@@ -0,0 +1,4 @@
+filetype: fms restart
+is restart: false
+datapath: ./anl/mem%{member}%
+filename_nonrestart: cubed_sphere_grid_atminc.jedi.nc
diff --git a/parm/jcb-gdas/model/atmosphere/atmosphere_output_ensemble_increments_gaussian.yaml.j2 b/parm/jcb-gdas/model/atmosphere/atmosphere_output_ensemble_increments_gaussian.yaml.j2
new file mode 100644
index 000000000..6d3d3b2af
--- /dev/null
+++ b/parm/jcb-gdas/model/atmosphere/atmosphere_output_ensemble_increments_gaussian.yaml.j2
@@ -0,0 +1,12 @@
+filetype: auxgrid
+gridtype: gaussian
+filename: {{atmosphere_ensemble_increment_prefix}}
+field io names:
+ eastward_wind: ugrd
+ northward_wind: vgrd
+ air_temperature: tmp
+ air_pressure_at_surface: pressfc
+ water_vapor_mixing_ratio_wrt_moist_air: spfh
+ cloud_liquid_ice: icmr
+ cloud_liquid_water: clwmr
+ ozone_mass_mixing_ratio: o3mr
diff --git a/parm/jcb-gdas/model/atmosphere/atmosphere_posterior_output_cubed_sphere.yaml.j2 b/parm/jcb-gdas/model/atmosphere/atmosphere_posterior_output_cubed_sphere.yaml.j2
new file mode 100644
index 000000000..aa72fc7e3
--- /dev/null
+++ b/parm/jcb-gdas/model/atmosphere/atmosphere_posterior_output_cubed_sphere.yaml.j2
@@ -0,0 +1,5 @@
+filetype: cube sphere history
+provider: ufs
+ufs soil nlev: 4
+ufs fields split by level: [smc,stc]
+filename: ./anl/{{ atmosphere_ensemble_analysis_prefix }}cubed_sphere_grid_atmanl.ensmean.nc
diff --git a/parm/jcb-gdas/model/atmosphere/atmosphere_posterior_output_gaussian.yaml.j2 b/parm/jcb-gdas/model/atmosphere/atmosphere_posterior_output_gaussian.yaml.j2
new file mode 100644
index 000000000..a14180d5f
--- /dev/null
+++ b/parm/jcb-gdas/model/atmosphere/atmosphere_posterior_output_gaussian.yaml.j2
@@ -0,0 +1,12 @@
+filetype: auxgrid
+gridtype: gaussian
+filename: {{atmosphere_posterior_output_gaussian}}
+field io names:
+ eastward_wind: ugrd
+ northward_wind: vgrd
+ air_temperature: tmp
+ air_pressure_at_surface: pressfc
+ water_vapor_mixing_ratio_wrt_moist_air: spfh
+ cloud_liquid_ice: icmr
+ cloud_liquid_water: clwmr
+ ozone_mass_mixing_ratio: o3mr
diff --git a/parm/jcb-gdas/model/marine/marine_3dfgat_outer_loop_1.yaml.j2 b/parm/jcb-gdas/model/marine/marine_3dfgat_outer_loop_1.yaml.j2
new file mode 100644
index 000000000..e90d9ddc0
--- /dev/null
+++ b/parm/jcb-gdas/model/marine/marine_3dfgat_outer_loop_1.yaml.j2
@@ -0,0 +1,8 @@
+- ninner: {{marine_ninner_1}}
+ gradient norm reduction: {{marine_grad_red_1}}
+ geometry:
+ geom_grid_file: ./anl_geom/soca_gridspec.nc
+ mom6_input_nml: ./anl_geom/mom_input.nml
+ fields metadata: {{marine_soca_files_path}}/fields_metadata.yaml
+ diagnostics:
+ departures: ombg
diff --git a/parm/jcb-gdas/model/marine/marine_background.yaml.j2 b/parm/jcb-gdas/model/marine/marine_background.yaml.j2
new file mode 100644
index 000000000..4be1f74fc
--- /dev/null
+++ b/parm/jcb-gdas/model/marine/marine_background.yaml.j2
@@ -0,0 +1,20 @@
+read_from_file: 1
+basename: {{ marine_background_path}}
+ocn_filename: MOM.res.nc
+ice_filename: cice.res.nc
+date: "{{ marine_background_time }}"
+state variables:
+- sea_ice_area_fraction
+- sea_ice_thickness
+- sea_ice_snow_thickness
+- snow_ice_surface_temperature
+- air_temperature
+- bulk_ice_salinity
+- sea_water_salinity
+- sea_water_potential_temperature
+#- eastward_sea_water_velocity
+#- northward_sea_water_velocity
+- sea_surface_height_above_geoid
+- sea_water_cell_thickness
+- ocean_mixed_layer_thickness
+- sea_water_depth
diff --git a/parm/jcb-gdas/model/marine/marine_background_ensemble.yaml.j2 b/parm/jcb-gdas/model/marine/marine_background_ensemble.yaml.j2
new file mode 100644
index 000000000..911cf80ac
--- /dev/null
+++ b/parm/jcb-gdas/model/marine/marine_background_ensemble.yaml.j2
@@ -0,0 +1,10 @@
+members from template:
+ template:
+ date: '{{ marine_window_middle_iso }}'
+ ocn_filename: "ocean.%mem%.nc"
+ ice_filename: "ice.%mem%.nc"
+ read_from_file: 1
+ basename: {{ marine_enspert_relpath }}/ens/
+ state variables: [sea_water_salinity, sea_water_potential_temperature, sea_surface_height_above_geoid, sea_water_cell_thickness, eastward_sea_water_velocity, northward_sea_water_velocity, sea_ice_area_fraction]
+ pattern: '%mem%'
+ nmembers: {{ marine_number_ensemble_members }}
diff --git a/parm/jcb-gdas/model/marine/marine_background_error_hybrid_diffusion_diffusion.yaml.j2 b/parm/jcb-gdas/model/marine/marine_background_error_hybrid_diffusion_diffusion.yaml.j2
new file mode 100644
index 000000000..6ff6713a4
--- /dev/null
+++ b/parm/jcb-gdas/model/marine/marine_background_error_hybrid_diffusion_diffusion.yaml.j2
@@ -0,0 +1,107 @@
+covariance model: hybrid
+components:
+- covariance:
+ covariance model: SABER
+ change background resolution: true
+ saber central block:
+ saber block name: diffusion
+ read:
+ groups:
+ - variables:
+ - sea_water_potential_temperature
+ - sea_water_salinity
+ - sea_surface_height_above_geoid
+ - sea_ice_area_fraction
+ horizontal:
+ filepath: ./staticb/hz_ocean
+ vertical:
+ levels: {{marine_vt_levels}}
+ filepath: ./staticb/vt_ocean
+ # TODO(G): OK to not use what's below but it will need
+ # to be fixed when we add ice thickness and
+ # snow depth
+ # - variables: [sea_ice_area_fraction]
+ # horizontal:
+ # filepath: ./staticb/hz_ice
+
+ saber outer blocks:
+ - saber block name: StdDev
+ read:
+ model file:
+ date: '{{marine_stddev_time}}'
+ basename: ./staticb/
+ ocn_filename: 'ocn.bkgerr_parametric_stddev.nc'
+ ice_filename: 'ice.bkgerr_parametric_stddev.nc'
+ read_from_file: 3
+ linear variable change:
+ input variables:
+ - sea_ice_area_fraction
+ - sea_ice_thickness
+ - sea_ice_snow_thickness
+ - sea_water_salinity
+ - sea_water_potential_temperature
+ #- eastward_sea_water_velocity
+ #- northward_sea_water_velocity
+ - sea_surface_height_above_geoid
+ output variables:
+ - sea_ice_area_fraction
+ - sea_ice_thickness
+ - sea_ice_snow_thickness
+ - sea_water_salinity
+ - sea_water_potential_temperature
+ #- eastward_sea_water_velocity
+ #- northward_sea_water_velocity
+ - sea_surface_height_above_geoid
+ linear variable changes:
+ - linear variable change name: BalanceSOCA
+ weight:
+ value: 1.00
+
+{% if marine_ensemble_b | default(false) %}
+- covariance:
+ covariance model: SABER
+ ensemble:
+ members from template:
+ template:
+ read_from_file: 1
+ date: '{{marine_stddev_time}}'
+ basename: ../ensdata/
+ ocn_filename: ocn.pert.%mem%.nc
+ ice_filename: ice.pert.%mem%.nc
+ state variables:
+ - sea_water_potential_temperature
+ - sea_water_salinity
+ #- eastward_sea_water_velocity
+ #- northward_sea_water_velocity
+ - sea_surface_height_above_geoid
+ - sea_ice_area_fraction
+ - sea_ice_thickness
+ - sea_ice_snow_thickness
+ pattern: '%mem%'
+ nmembers: '{{marine_number_ensemble_members}}'
+ saber central block:
+ saber block name: Ensemble
+ localization:
+ saber central block:
+ saber block name: diffusion
+ read:
+ groups:
+ - variables:
+ - sea_water_potential_temperature
+ - sea_water_salinity
+ - sea_surface_height_above_geoid
+ - sea_ice_area_fraction
+ multivariate strategy: duplicated
+ horizontal:
+ filepath: ./staticb/hz_ocean
+ vertical:
+ strategy: duplicated
+
+ weight:
+ read_from_file: 3
+ basename: ./
+ ocn_filename: 'ocean.ens_weights.nc'
+ ice_filename: 'ice.ens_weights.nc'
+ date: '{{marine_stddev_time}}'
+{% endif %}
+
diff --git a/parm/jcb-gdas/model/marine/marine_background_error_static_diffusion.yaml.j2 b/parm/jcb-gdas/model/marine/marine_background_error_static_diffusion.yaml.j2
new file mode 100644
index 000000000..0d663c57f
--- /dev/null
+++ b/parm/jcb-gdas/model/marine/marine_background_error_static_diffusion.yaml.j2
@@ -0,0 +1,72 @@
+covariance model: SABER
+change background resolution: true
+saber central block:
+ saber block name: diffusion
+ read:
+ groups:
+ - variables:
+ - sea_water_potential_temperature
+ - sea_water_salinity
+ - sea_surface_height_above_geoid
+ - sea_ice_area_fraction
+ horizontal:
+ filepath: ./staticb/hz_ocean
+ vertical:
+ levels: {{marine_vt_levels}}
+ filepath: ./staticb/vt_ocean
+# TODO(G): OK to not use what's below but it will need
+# to be fixed when we add ice thickness and
+# snow depth
+# - variables: [sea_ice_area_fraction]
+# horizontal:
+# filepath: ./staticb/hz_ice
+
+saber outer blocks:
+- saber block name: StdDev
+ read:
+ model file:
+ date: '{{marine_stddev_time}}'
+ basename: ./staticb/
+ ocn_filename: 'ocn.bkgerr_parametric_stddev.nc'
+ ice_filename: 'ice.bkgerr_parametric_stddev.nc'
+ read_from_file: 3
+
+#- saber block name: MLBalance
+# geometry:
+# mom6_input_nml: mom_input.nml
+# fields metadata: ./fields_metadata.yaml
+# ML Balances:
+# arctic:
+# ffnn:
+# inputSize: 7
+# outputSize: 1
+# hiddenSize: 2
+# load model: /work/noaa/da/gvernier/ai/runs/arctic.pt
+# antarctic:
+# ffnn:
+# inputSize: 7
+# outputSize: 1
+# hiddenSize: 2
+# load model: /work/noaa/da/gvernier/ai/runs/antarctic.pt
+
+linear variable change:
+ input variables:
+ - sea_ice_area_fraction
+ - sea_ice_thickness
+ - sea_ice_snow_thickness
+ - sea_water_salinity
+ - sea_water_potential_temperature
+ #- eastward_sea_water_velocity
+ #- northward_sea_water_velocity
+ - sea_surface_height_above_geoid
+ output variables:
+ - sea_ice_area_fraction
+ - sea_ice_thickness
+ - sea_ice_snow_thickness
+ - sea_water_salinity
+ - sea_water_potential_temperature
+ #- eastward_sea_water_velocity
+ #- northward_sea_water_velocity
+ - sea_surface_height_above_geoid
+ linear variable changes:
+ - linear variable change name: BalanceSOCA
diff --git a/parm/jcb-gdas/model/marine/marine_final_increment.yaml.j2 b/parm/jcb-gdas/model/marine/marine_final_increment.yaml.j2
new file mode 100644
index 000000000..ead7a3ed1
--- /dev/null
+++ b/parm/jcb-gdas/model/marine/marine_final_increment.yaml.j2
@@ -0,0 +1,9 @@
+output:
+ state component:
+ datadir: {{marine_final_increment_dir}}
+ date: '{{marine_window_begin}}'
+ exp: {{marine_final_increment_exp}}
+ type: incr
+geometry:
+ mom6_input_nml: mom_input.nml
+ fields metadata: {{marine_soca_files_path}}/fields_metadata.yaml
diff --git a/parm/jcb-gdas/model/marine/marine_geometry_background.yaml.j2 b/parm/jcb-gdas/model/marine/marine_geometry_background.yaml.j2
new file mode 100644
index 000000000..2ab3b6789
--- /dev/null
+++ b/parm/jcb-gdas/model/marine/marine_geometry_background.yaml.j2
@@ -0,0 +1,2 @@
+mom6_input_nml: mom_input.nml
+fields metadata: {{marine_soca_files_path}}/fields_metadata.yaml
diff --git a/parm/jcb-gdas/model/marine/marine_model_pseudo.yaml.j2 b/parm/jcb-gdas/model/marine/marine_model_pseudo.yaml.j2
new file mode 100644
index 000000000..9188340bb
--- /dev/null
+++ b/parm/jcb-gdas/model/marine/marine_model_pseudo.yaml.j2
@@ -0,0 +1,10 @@
+name: PseudoModel
+tstep: {{marine_forecast_timestep}}
+states:
+{% for marine_pseudo_model_state in marine_pseudo_model_states %}
+- date: '{{ marine_pseudo_model_state.date }}'
+ basename: '{{ marine_pseudo_model_state.basename }}'
+ ocn_filename: '{{ marine_pseudo_model_state.ocn_filename }}'
+ ice_filename: '{{ marine_pseudo_model_state.ice_filename }}'
+ read_from_file: {{ marine_pseudo_model_state.read_from_file }}
+{% endfor %}
diff --git a/parm/jcb-gdas/model/marine/marine_output.yaml.j2 b/parm/jcb-gdas/model/marine/marine_output.yaml.j2
new file mode 100644
index 000000000..2c8e2adb9
--- /dev/null
+++ b/parm/jcb-gdas/model/marine/marine_output.yaml.j2
@@ -0,0 +1,4 @@
+datadir: {{marine_output_dir}}
+exp: {{marine_output_exp}}
+type: an
+frequency: {{marine_output_freq}}
diff --git a/parm/jcb-gdas/model/marine/marine_output_increment.yaml.j2 b/parm/jcb-gdas/model/marine/marine_output_increment.yaml.j2
new file mode 100644
index 000000000..4cae31926
--- /dev/null
+++ b/parm/jcb-gdas/model/marine/marine_output_increment.yaml.j2
@@ -0,0 +1,4 @@
+datadir: letkf_output/
+date: '{{ marine_window_begin_iso }}'
+exp: letkf.inc
+type: ens
diff --git a/parm/jcb-gdas/model/marine/marine_output_mean_prior.yaml.j2 b/parm/jcb-gdas/model/marine/marine_output_mean_prior.yaml.j2
new file mode 100644
index 000000000..20fedd4c5
--- /dev/null
+++ b/parm/jcb-gdas/model/marine/marine_output_mean_prior.yaml.j2
@@ -0,0 +1,4 @@
+datadir: letkf_output/
+date: '{{ marine_window_begin_iso }}'
+exp: letkf.mean_prior
+type: fc
diff --git a/parm/jcb-gdas/model/marine/marine_output_variance_posterior.yaml.j2 b/parm/jcb-gdas/model/marine/marine_output_variance_posterior.yaml.j2
new file mode 100644
index 000000000..734344d98
--- /dev/null
+++ b/parm/jcb-gdas/model/marine/marine_output_variance_posterior.yaml.j2
@@ -0,0 +1,4 @@
+datadir: letkf_output/
+date: '{{ marine_window_begin_iso }}'
+exp: letkf.var_post
+type: an
diff --git a/parm/jcb-gdas/model/marine/marine_output_variance_prior.yaml.j2 b/parm/jcb-gdas/model/marine/marine_output_variance_prior.yaml.j2
new file mode 100644
index 000000000..de97f917c
--- /dev/null
+++ b/parm/jcb-gdas/model/marine/marine_output_variance_prior.yaml.j2
@@ -0,0 +1,4 @@
+datadir: letkf_output/
+date: '{{ marine_window_begin_iso }}'
+exp: letkf.var_prior
+type: fc
diff --git a/parm/jcb-gdas/model/marine/marine_posterior_output.yaml.j2 b/parm/jcb-gdas/model/marine/marine_posterior_output.yaml.j2
new file mode 100644
index 000000000..fc823ea8d
--- /dev/null
+++ b/parm/jcb-gdas/model/marine/marine_posterior_output.yaml.j2
@@ -0,0 +1,4 @@
+datadir: letkf_output/
+date: '{{ marine_window_begin_iso }}'
+exp: letkf
+type: ens
diff --git a/parm/jcb-gdas/model/snow/snow_3dvar_outer_loop_1.yaml.j2 b/parm/jcb-gdas/model/snow/snow_3dvar_outer_loop_1.yaml.j2
new file mode 100644
index 000000000..53085b711
--- /dev/null
+++ b/parm/jcb-gdas/model/snow/snow_3dvar_outer_loop_1.yaml.j2
@@ -0,0 +1,29 @@
+- ninner: 50
+ gradient norm reduction: 1e-10
+ test: on
+ geometry:
+ fms initialization:
+ namelist filename: {{ snow_fv3jedi_files_path }}/fmsmpp.nml
+ field table filename: {{ snow_fv3jedi_files_path }}/field_table
+ akbk: {{ snow_fv3jedi_files_path }}/akbk.nc4
+ layout:
+ - {{ snow_layout_x }}
+ - {{ snow_layout_y }}
+ npx: {{ snow_npx_anl }}
+ npy: {{ snow_npy_anl }}
+ npz: {{ snow_npz_anl }}
+ time invariant fields:
+ state fields:
+ datetime: '{{ snow_background_time_iso }}'
+ filetype: fms restart
+ skip coupler file: true
+ state variables:
+ - filtered_orography
+ - fraction_of_land
+ field io names:
+ filtered_orography: orog_filt
+ fraction_of_land: land_frac
+ datapath: {{ snow_orog_files_path }}/
+ filename_orog: {{ snow_orog_prefix }}_oro_data.nc
+ diagnostics:
+ departures: bkgmob
diff --git a/parm/jcb-gdas/model/snow/snow_background.yaml.j2 b/parm/jcb-gdas/model/snow/snow_background.yaml.j2
new file mode 100644
index 000000000..1f1ccb57b
--- /dev/null
+++ b/parm/jcb-gdas/model/snow/snow_background.yaml.j2
@@ -0,0 +1,21 @@
+datapath: {{ snow_background_path }}
+filetype: fms restart
+skip coupler file: true
+datetime: '{{ snow_background_time_iso }}'
+state variables:
+- totalSnowDepth
+- vtype
+- slmsk
+- sheleg
+- filtered_orography
+- fraction_of_ice
+- fraction_of_land
+- stc
+field io names:
+ totalSnowDepth: snodl
+ filtered_orography: orog_filt
+ fraction_of_ice: fice
+ fraction_of_land: land_frac
+filename_sfcd: '{{ snow_background_time_fv3 }}.sfc_data.nc'
+filename_cplr: '{{ snow_background_time_fv3 }}.coupler.res'
+filename_orog: '{{ snow_orog_prefix }}_oro_data.nc'
diff --git a/parm/jcb-gdas/model/snow/snow_background_error.yaml.j2 b/parm/jcb-gdas/model/snow/snow_background_error.yaml.j2
new file mode 100644
index 000000000..3d853038a
--- /dev/null
+++ b/parm/jcb-gdas/model/snow/snow_background_error.yaml.j2
@@ -0,0 +1,47 @@
+covariance model: SABER
+saber central block:
+ saber block name: BUMP_NICAS
+ read:
+ general:
+ universe length-scale: 300000.0
+ drivers:
+ multivariate strategy: univariate
+ read global nicas: true
+ nicas:
+ explicit length-scales: true
+ horizontal length-scale:
+ - groups:
+ - totalSnowDepth_shadowLevels
+ value: 250000.0
+ vertical length-scale:
+ - groups:
+ - totalSnowDepth_shadowLevels
+ value: 0.0
+ interpolation type:
+ - groups:
+ - totalSnowDepth_shadowLevels
+ type: c0
+ same horizontal convolution: true
+ io:
+ data directory: {{snow_bump_data_directory}}
+ files prefix: snow_bump_nicas_250km_shadowlevels
+saber outer blocks:
+- saber block name: ShadowLevels
+ fields metadata:
+ totalSnowDepth:
+ vert_coord: filtered_orography
+ calibration:
+ number of shadow levels: 50
+ lowest shadow level: -450.0
+ highest shadow level: 8850.0
+ vertical length-scale: 2000.0
+- saber block name: BUMP_StdDev
+ read:
+ drivers:
+ compute variance: true
+ variance:
+ explicit stddev: true
+ stddev:
+ - variables:
+ - totalSnowDepth
+ value: 30.0
diff --git a/parm/jcb-gdas/model/snow/snow_final_increment_fms.yaml.j2 b/parm/jcb-gdas/model/snow/snow_final_increment_fms.yaml.j2
new file mode 100644
index 000000000..7c9e13e23
--- /dev/null
+++ b/parm/jcb-gdas/model/snow/snow_final_increment_fms.yaml.j2
@@ -0,0 +1,24 @@
+output:
+ state component:
+ datapath: ./anl
+ prefix: snowinc
+ filetype: fms restart
+ filename_sfcd: '{{ snow_background_time_fv3 }}.sfc_data.nc'
+ filename_cplr: '{{ snow_background_time_fv3 }}.coupler.res'
+ state variables:
+ - totalSnowDepth
+ - vtype
+ - slmsk
+ field io names:
+ totalSnowDepth: snodl
+geometry:
+ fms initialization:
+ namelist filename: "{{ snow_fv3jedi_files_path }}/fmsmpp.nml"
+ field table filename: "{{ snow_fv3jedi_files_path }}/field_table"
+ akbk: "{{ snow_fv3jedi_files_path }}/akbk.nc4"
+ layout:
+ - {{ snow_layout_x }}
+ - {{ snow_layout_y }}
+ npx: {{ snow_npx_ges }}
+ npy: {{ snow_npy_ges }}
+ npz: {{ snow_npz_ges }}
diff --git a/parm/jcb-gdas/model/snow/snow_geometry_background.yaml.j2 b/parm/jcb-gdas/model/snow/snow_geometry_background.yaml.j2
new file mode 100644
index 000000000..ff72e6222
--- /dev/null
+++ b/parm/jcb-gdas/model/snow/snow_geometry_background.yaml.j2
@@ -0,0 +1,10 @@
+fms initialization:
+ namelist filename: "{{snow_fv3jedi_files_path}}/fmsmpp.nml"
+ field table filename: "{{snow_fv3jedi_files_path}}/field_table"
+akbk: "{{snow_fv3jedi_files_path}}/akbk.nc4"
+layout:
+- {{snow_layout_x}}
+- {{snow_layout_y}}
+npx: {{snow_npx_ges}}
+npy: {{snow_npy_ges}}
+npz: {{snow_npz_ges}}
diff --git a/parm/jcb-gdas/model/soil/soil_3dvar_outer_loop_1.yaml.j2 b/parm/jcb-gdas/model/soil/soil_3dvar_outer_loop_1.yaml.j2
new file mode 100644
index 000000000..302fd4a33
--- /dev/null
+++ b/parm/jcb-gdas/model/soil/soil_3dvar_outer_loop_1.yaml.j2
@@ -0,0 +1,29 @@
+- ninner: 50
+ gradient norm reduction: 1e-10
+ test: on
+ geometry:
+ fms initialization:
+ namelist filename: {{ soil_fv3jedi_files_path }}/fmsmpp.nml
+ field table filename: {{ soil_fv3jedi_files_path }}/field_table
+ akbk: {{ soil_fv3jedi_files_path }}/akbk.nc4
+ layout:
+ - {{ soil_layout_x }}
+ - {{ soil_layout_y }}
+ npx: {{ soil_npx_anl }}
+ npy: {{ soil_npy_anl }}
+ npz: {{ soil_npz_anl }}
+ time invariant fields:
+ state fields:
+ datetime: '{{ soil_background_time_iso }}'
+ filetype: fms restart
+ skip coupler file: true
+ state variables:
+ - filtered_orography
+ - fraction_of_land
+ field io names:
+ filtered_orography: orog_filt
+ fraction_of_land: land_frac
+ datapath: {{ soil_orog_files_path }}/
+ filename_orog: {{ soil_orog_prefix }}_oro_data.nc
+ diagnostics:
+ departures: bkgmob
diff --git a/parm/jcb-gdas/model/soil/soil_background.yaml.j2 b/parm/jcb-gdas/model/soil/soil_background.yaml.j2
new file mode 100644
index 000000000..c495e93f9
--- /dev/null
+++ b/parm/jcb-gdas/model/soil/soil_background.yaml.j2
@@ -0,0 +1,23 @@
+datapath: {{ soil_background_path }}
+filetype: fms restart
+skip coupler file: true
+datetime: '{{ soil_background_time_iso }}'
+state variables:
+- soilMoistureVolumetric
+- stc
+- totalSnowDepth
+- sheleg
+- vtype
+- slmsk
+- filtered_orography
+- fraction_of_ice
+- fraction_of_land
+field io names:
+ soilMoistureVolumetric: smc
+ totalSnowDepth: snodl
+ filtered_orography: orog_filt
+ fraction_of_ice: fice
+ fraction_of_land: land_frac
+filename_sfcd: '{{ soil_background_time_fv3 }}.sfc_data.nc'
+filename_cplr: '{{ soil_background_time_fv3 }}.coupler.res'
+filename_orog: '{{ soil_orog_prefix }}_oro_data.nc'
diff --git a/parm/jcb-gdas/model/soil/soil_background_error.yaml.j2 b/parm/jcb-gdas/model/soil/soil_background_error.yaml.j2
new file mode 100644
index 000000000..c1220bea3
--- /dev/null
+++ b/parm/jcb-gdas/model/soil/soil_background_error.yaml.j2
@@ -0,0 +1,40 @@
+covariance model: SABER
+saber central block:
+ saber block name: BUMP_NICAS
+ calibration: #read:
+ general:
+ universe length-scale: 5000000.0
+ drivers:
+ multivariate strategy: univariate
+ compute nicas: true #read global nicas: true
+ write global nicas: true
+ nicas:
+ resolution: 4
+ explicit length-scales: true
+ horizontal length-scale:
+ - groups:
+ - soilMoistureVolumetric
+ value: 1000000.0
+ vertical length-scale:
+ - groups:
+ - soilMoistureVolumetric
+ value: 1500.0
+ interpolation type:
+ - groups:
+ - soilMoistureVolumetric
+ type: c0
+ same horizontal convolution: true
+ io:
+ data directory: ./berror
+ files prefix: smc_bump_nicas_1000km_{{ soil_background_time_fv3 }}
+saber outer blocks:
+- saber block name: BUMP_StdDev
+ read:
+ drivers:
+ compute variance: true
+ variance:
+ explicit stddev: true
+ stddev:
+ - variables:
+ - soilMoistureVolumetric
+ value: 0.2
diff --git a/parm/jcb-gdas/model/soil/soil_final_increment_fms.yaml.j2 b/parm/jcb-gdas/model/soil/soil_final_increment_fms.yaml.j2
new file mode 100644
index 000000000..b3a7f22f8
--- /dev/null
+++ b/parm/jcb-gdas/model/soil/soil_final_increment_fms.yaml.j2
@@ -0,0 +1,28 @@
+output:
+ state component:
+ datapath: ./anl
+ prefix: soilinc
+ filetype: fms restart
+ filename_sfcd: '{{ soil_background_time_fv3 }}.sfc_data.nc'
+ filename_cplr: '{{ soil_background_time_fv3 }}.coupler.res'
+ state variables:
+ - soilMoistureVolumetric
+ - stc
+ - totalSnowDepth
+ - sheleg
+ - vtype
+ - slmsk
+ field io names:
+ soilMoistureVolumetric: smc
+ totalSnowDepth: snodl
+geometry:
+ fms initialization:
+ namelist filename: "{{ soil_fv3jedi_files_path }}/fmsmpp.nml"
+ field table filename: "{{ soil_fv3jedi_files_path }}/field_table"
+ akbk: "{{ soil_fv3jedi_files_path }}/akbk.nc4"
+ layout:
+ - {{ soil_layout_x }}
+ - {{ soil_layout_y }}
+ npx: {{ soil_npx_ges }}
+ npy: {{ soil_npy_ges }}
+ npz: {{ soil_npz_ges }}
diff --git a/parm/jcb-gdas/model/soil/soil_geometry_background.yaml.j2 b/parm/jcb-gdas/model/soil/soil_geometry_background.yaml.j2
new file mode 100644
index 000000000..d60dc8a36
--- /dev/null
+++ b/parm/jcb-gdas/model/soil/soil_geometry_background.yaml.j2
@@ -0,0 +1,10 @@
+fms initialization:
+ namelist filename: "{{soil_fv3jedi_files_path}}/fmsmpp.nml"
+ field table filename: "{{soil_fv3jedi_files_path}}/field_table"
+akbk: "{{soil_fv3jedi_files_path}}/akbk.nc4"
+layout:
+- {{soil_layout_x}}
+- {{soil_layout_y}}
+npx: {{soil_npx_ges}}
+npy: {{soil_npy_ges}}
+npz: {{soil_npz_ges}}
diff --git a/parm/jcb-gdas/model/soil/soil_output.yaml.j2 b/parm/jcb-gdas/model/soil/soil_output.yaml.j2
new file mode 100644
index 000000000..83e44b6ee
--- /dev/null
+++ b/parm/jcb-gdas/model/soil/soil_output.yaml.j2
@@ -0,0 +1,23 @@
+state variables:
+- soilMoistureVolumetric
+- stc
+- totalSnowDepth
+- sheleg
+- vtype
+- slmsk
+- filtered_orography
+- fraction_of_ice
+- fraction_of_land
+field io names:
+ soilMoistureVolumetric: smc
+ totalSnowDepth: snodl
+ filtered_orography: orog_filt
+ fraction_of_ice: fice
+ fraction_of_land: land_frac
+datapath: ./anl
+prefix: soil_finanl
+filetype: fms restart
+datetime: '{{ soil_background_time_iso }}'
+filename_sfcd: '{{ soil_background_time_fv3 }}.sfc_data.nc'
+filename_cplr: '{{ soil_background_time_fv3 }}.coupler.res'
+filename_orog: '{{ soil_orog_prefix }}_oro_data.nc'
diff --git a/parm/jcb-gdas/observation_chronicle/snow/t00z/adpsfc_snow.yaml b/parm/jcb-gdas/observation_chronicle/snow/t00z/adpsfc_snow.yaml
new file mode 100644
index 000000000..cc3d8d944
--- /dev/null
+++ b/parm/jcb-gdas/observation_chronicle/snow/t00z/adpsfc_snow.yaml
@@ -0,0 +1,38 @@
+# Instrument metadata
+# -------------------
+commissioned: 1970-01-01T00:00:00
+
+observer_type: conventional # Type of chronicle to use
+
+window_option: max
+
+# observation type initial configuration
+# --------------------------------
+stations_to_reject: [71120, 71397, 71621, 71727, 71816 # from North America
+ , 71641, 71976, 71743, 71902
+ , 10863, 16179 # from Europe for unrealistic snow presence during summer
+ , 40550, 40580, 40582, 40587, 40592 # from Mid East for unrealistic snow values
+ , 47005, 47008, 47014, 47016, 47020, 47022, 47025, 47028, 47031, 47035 # from North Korea
+ , 47037, 47039, 47041, 47046, 47050, 47052, 47055, 47058, 47060, 47061
+ , 47065, 47067, 47068, 47069, 47070, 47069, 47070, 47075, 47090
+ , 48698, 48830 # from Singapore
+ # Snow reports with frequent incorrect zero values and snow presence during summer from China
+ , 50136, 50603, 50953, 50968, 52955, 55696, 56004, 56146, 56357, 56586 # China
+ , 65250] # from Africa
+
+# Chronicle of changes for this observation type
+# ----------------------------------------
+chronicles:
+
+- action_date: "2021-10-01T00:00:00"
+ justification: 'These stations are okay from this time'
+ remove_from_reject_list: [71120, 71397, 71727, 71816]
+
+- action_date: "2022-10-01T00:00:00"
+ justification: 'These stations are okay from this time'
+ remove_from_reject_list: [50136, 50603, 50953, 50968, 52955, 55696
+ , 56004, 56146, 56357, 56586]
+
+- action_date: "2022-10-01T01:00:00"
+ justification: 'Add to reject these stations'
+ add_to_reject_list: [47095, 47098, 47101, 47102]
diff --git a/parm/jcb-gdas/observation_chronicle/snow/t00z/ghcn_snow.yaml b/parm/jcb-gdas/observation_chronicle/snow/t00z/ghcn_snow.yaml
new file mode 100644
index 000000000..20420eabd
--- /dev/null
+++ b/parm/jcb-gdas/observation_chronicle/snow/t00z/ghcn_snow.yaml
@@ -0,0 +1,14 @@
+# Instrument metadata
+# -------------------
+commissioned: 1900-01-01T00:00:00
+
+observer_type: conventional # Type of chronicle to use
+
+window_option: max
+
+# observation type initial configuration
+# --------------------------------
+stations_to_reject: [fakelist]
+
+# Chronicle of changes for this observation type
+# ----------------------------------------
diff --git a/parm/jcb-gdas/observation_chronicle/snow/t00z/madis_snow.yaml b/parm/jcb-gdas/observation_chronicle/snow/t00z/madis_snow.yaml
new file mode 100644
index 000000000..3171740d6
--- /dev/null
+++ b/parm/jcb-gdas/observation_chronicle/snow/t00z/madis_snow.yaml
@@ -0,0 +1,15 @@
+# Instrument metadata
+# -------------------
+commissioned: 2021-01-01T00:00:00
+decommissioned: 2023-05-31T18:00:00
+
+observer_type: conventional # Type of chronicle to use
+
+window_option: max
+
+# observation type initial configuration
+# --------------------------------
+stations_to_reject: [BF001, BF002, BF004, BF009, BF010, BF012, BF017, BF019, BF030, BF034, BF035, BF036, BF037, BF038, BF044, BF049, BF052, BF054, BF056, BF059, BF061, BF066, BF069, BF078, BF080, BF084, BF086, BF089, BF091, BF110, BF117, BF121, BF122, BF123, BF132, BF137, BF142, BF143, BF150, BF151, BF159, BF191, BF197, BF209, BF215, BF233, BF234, BF235, BF242, BF284, BOWC1, BT007, BT008, BT116, BT117, BT119, BT128, BT140, CAAXM, CAINP, CALXV, CSNA2, FAFA2, HPN06, KESQ6, LACQ6, LPTUT, MKLA2, OHAW1, OJIM4, OKEQ6, SHDA2, TUNA2, UTRMD, WEAQ6, WINM4, XACC1]
+
+# Chronicle of changes for this observation type
+# ----------------------------------------
diff --git a/parm/jcb-gdas/observation_chronicle/snow/t00z/sfcsno.yaml b/parm/jcb-gdas/observation_chronicle/snow/t00z/sfcsno.yaml
new file mode 100644
index 000000000..cc3d8d944
--- /dev/null
+++ b/parm/jcb-gdas/observation_chronicle/snow/t00z/sfcsno.yaml
@@ -0,0 +1,38 @@
+# Instrument metadata
+# -------------------
+commissioned: 1970-01-01T00:00:00
+
+observer_type: conventional # Type of chronicle to use
+
+window_option: max
+
+# observation type initial configuration
+# --------------------------------
+stations_to_reject: [71120, 71397, 71621, 71727, 71816 # from North America
+ , 71641, 71976, 71743, 71902
+ , 10863, 16179 # from Europe for unrealistic snow presence during summer
+ , 40550, 40580, 40582, 40587, 40592 # from Mid East for unrealistic snow values
+ , 47005, 47008, 47014, 47016, 47020, 47022, 47025, 47028, 47031, 47035 # from North Korea
+ , 47037, 47039, 47041, 47046, 47050, 47052, 47055, 47058, 47060, 47061
+ , 47065, 47067, 47068, 47069, 47070, 47069, 47070, 47075, 47090
+ , 48698, 48830 # from Singapore
+ # Snow reports with frequent incorrect zero values and snow presence during summer from China
+ , 50136, 50603, 50953, 50968, 52955, 55696, 56004, 56146, 56357, 56586 # China
+ , 65250] # from Africa
+
+# Chronicle of changes for this observation type
+# ----------------------------------------
+chronicles:
+
+- action_date: "2021-10-01T00:00:00"
+ justification: 'These stations are okay from this time'
+ remove_from_reject_list: [71120, 71397, 71727, 71816]
+
+- action_date: "2022-10-01T00:00:00"
+ justification: 'These stations are okay from this time'
+ remove_from_reject_list: [50136, 50603, 50953, 50968, 52955, 55696
+ , 56004, 56146, 56357, 56586]
+
+- action_date: "2022-10-01T01:00:00"
+ justification: 'Add to reject these stations'
+ add_to_reject_list: [47095, 47098, 47101, 47102]
diff --git a/parm/jcb-gdas/observation_chronicle/snow/t00z/snocvr.yaml b/parm/jcb-gdas/observation_chronicle/snow/t00z/snocvr.yaml
new file mode 100644
index 000000000..0749e56ef
--- /dev/null
+++ b/parm/jcb-gdas/observation_chronicle/snow/t00z/snocvr.yaml
@@ -0,0 +1,14 @@
+# Instrument metadata
+# -------------------
+commissioned: 2023-05-01T00:00:00
+
+observer_type: conventional # Type of chronicle to use
+
+window_option: max
+
+# observation type initial configuration
+# --------------------------------
+stations_to_reject: [BFTU1, FRDN5, MWDO3, SGNN5, NUTA3, CNDA3, HBEA3, ELCN5]
+
+# Chronicle of changes for this observation type
+# ----------------------------------------
diff --git a/parm/jcb-gdas/observation_chronicle/snow/t00z/snocvr_snomad.yaml b/parm/jcb-gdas/observation_chronicle/snow/t00z/snocvr_snomad.yaml
new file mode 100644
index 000000000..41b3ed06c
--- /dev/null
+++ b/parm/jcb-gdas/observation_chronicle/snow/t00z/snocvr_snomad.yaml
@@ -0,0 +1,14 @@
+# Instrument metadata
+# -------------------
+commissioned: 2023-05-01T00:00:00
+
+observer_type: conventional # Type of chronicle to use
+
+window_option: max
+
+# observation type initial configuration
+# --------------------------------
+stations_to_reject: [fakelist]
+
+# Chronicle of changes for this observation type
+# ----------------------------------------
diff --git a/parm/jcb-gdas/observation_chronicle/snow/t00z/snomad.yaml b/parm/jcb-gdas/observation_chronicle/snow/t00z/snomad.yaml
new file mode 100644
index 000000000..9db6e445d
--- /dev/null
+++ b/parm/jcb-gdas/observation_chronicle/snow/t00z/snomad.yaml
@@ -0,0 +1,14 @@
+# Instrument metadata
+# -------------------
+commissioned: 2024-11-01T00:00:00
+
+observer_type: conventional # Type of chronicle to use
+
+window_option: max
+
+# observation type initial configuration
+# --------------------------------
+stations_to_reject: [fakelist]
+
+# Chronicle of changes for this observation type
+# ----------------------------------------
diff --git a/parm/jcb-gdas/observation_chronicle/snow/t06z/adpsfc_snow.yaml b/parm/jcb-gdas/observation_chronicle/snow/t06z/adpsfc_snow.yaml
new file mode 100644
index 000000000..4f4ff7be9
--- /dev/null
+++ b/parm/jcb-gdas/observation_chronicle/snow/t06z/adpsfc_snow.yaml
@@ -0,0 +1,78 @@
+# Instrument metadata
+# -------------------
+commissioned: 1970-01-01T00:00:00
+
+observer_type: conventional # Type of chronicle to use
+
+window_option: max
+
+# observation type initial configuration
+# --------------------------------
+stations_to_reject: [71120, 71397, 71621, 71727, 71816 # from North America
+ , 71641, 71976, 71743, 71902
+ , 10863, 16179 # from Europe
+ , 40550, 40580, 40582, 40587, 40592 # Mid East
+ , 47005, 47008, 47014, 47016, 47020, 47022, 47025, 47028, 47031, 47035 # from North Korea
+ , 47037, 47039, 47041, 47046, 47050, 47052, 47055, 47058, 47060, 47061
+ , 47065, 47067, 47068, 47069, 47070, 47069, 47070, 47075, 47090
+ , 48698, 48830 # from Singapore
+ # Snow reports with frequent incorrect zero values in 06/12/18z cycles from China
+ , 50136, 50353, 50468, 50557, 50564, 50603, 50658, 50745, 50756, 50774 # from China
+ , 50788, 50844, 50854, 50888, 50949, 50953, 50963, 50968, 50978, 50983
+ , 51467, 51573, 51644, 51656, 51716, 51747, 51765, 51777, 51828, 51886
+ , 52203, 52267, 52323, 52418, 52436, 52533, 52652, 52681, 52713, 52754
+ , 52818, 52836, 52866, 52908, 52955, 52983, 53068, 53083, 53149, 53192
+ , 53231, 53276, 53336, 53352, 53391, 53463, 53480, 53487, 53502, 53513
+ , 53529, 53543, 53564, 53588, 53593, 53614, 53646, 53673, 53698, 53705
+ , 53723, 53764, 53772, 53787, 53798, 53845, 53863, 53898, 53915, 53923
+ , 53959, 53975, 54026, 54027, 54049, 54094, 54096, 54115, 54135, 54157
+ , 54161, 54186, 54208, 54218, 54226, 54236, 54259, 54273, 54292, 54308
+ , 54311, 54324, 54337, 54342, 54346, 54374, 54377, 54386, 54401, 54405
+ , 54423, 54436, 54471, 54493, 54497, 54511, 54527, 54534, 54539, 54602
+ , 54618, 54662, 54715, 54725, 54751, 54753, 54776, 54808, 54823, 54826
+ , 54836, 54843, 54857, 54863, 54909, 54916, 54929, 55279, 55472, 55578
+ , 55591, 55664, 55696, 55773, 56004, 56033, 56065, 56096, 56106, 56116
+ , 56137, 56146, 56172, 56182, 56257, 56357, 56374, 56586, 56691, 57014
+ , 57046, 57067, 57071, 57083, 57259, 57265, 57279, 57297, 57378, 57399
+ , 57461, 57476, 57494, 57554, 57584, 57655, 57707, 57712, 57731, 57745
+ , 57766, 57776, 57793, 57799, 57832, 57845, 57853, 57866, 57902, 57922
+ , 58027, 58141, 58150, 58208, 58265, 58345, 58437, 58477, 58506, 58543
+ , 58556, 58569, 58633, 58652, 58725, 58730, 58731, 58752
+ , 65250] # from Africa
+
+# Chronicle of changes for this observation type
+# ----------------------------------------
+chronicles:
+
+- action_date: "2021-10-01T00:00:00"
+ justification: 'These stations are okay from this time'
+ remove_from_reject_list: [71120, 71397, 71727, 71816]
+
+- action_date: "2022-10-01T00:00:00"
+ justification: 'These stations are okay from this time'
+ remove_from_reject_list: [50136
+ , 50353, 50468, 50557, 50564, 50603, 50658, 50745, 50756, 50774 # from China
+ , 50788, 50844, 50854, 50888, 50949, 50953, 50963, 50968, 50978, 50983
+ , 51467, 51573, 51644, 51656, 51716, 51747, 51765, 51777, 51828, 51886
+ , 52203, 52267, 52323, 52418, 52436, 52533, 52652, 52681, 52713, 52754
+ , 52818, 52836, 52866, 52908, 52955, 52983, 53068, 53083, 53149, 53192
+ , 53231, 53276, 53336, 53352, 53391, 53463, 53480, 53487, 53502, 53513
+ , 53529, 53543, 53564, 53588, 53593, 53614, 53646, 53673, 53698, 53705
+ , 53723, 53764, 53772, 53787, 53798, 53845, 53863, 53898, 53915, 53923
+ , 53959, 53975, 54026, 54027, 54049, 54094, 54096, 54115, 54135, 54157
+ , 54161, 54186, 54208, 54218, 54226, 54236, 54259, 54273, 54292, 54308
+ , 54311, 54324, 54337, 54342, 54346, 54374, 54377, 54386, 54401, 54405
+ , 54423, 54436, 54471, 54493, 54497, 54511, 54527, 54534, 54539, 54602
+ , 54618, 54662, 54715, 54725, 54751, 54753, 54776, 54808, 54823, 54826
+ , 54836, 54843, 54857, 54863, 54909, 54916, 54929, 55279, 55472, 55578
+ , 55591, 55664, 55696, 55773, 56004, 56033, 56065, 56096, 56106, 56116
+ , 56137, 56146, 56172, 56182, 56257, 56357, 56374, 56586, 56691, 57014
+ , 57046, 57067, 57071, 57083, 57259, 57265, 57279, 57297, 57378, 57399
+ , 57461, 57476, 57494, 57554, 57584, 57655, 57707, 57712, 57731, 57745
+ , 57766, 57776, 57793, 57799, 57832, 57845, 57853, 57866, 57902, 57922
+ , 58027, 58141, 58150, 58208, 58265, 58345, 58437, 58477, 58506, 58543
+ , 58556, 58569, 58633, 58652, 58725, 58730, 58731, 58752]
+
+- action_date: "2022-10-01T01:00:00"
+ justification: 'Add to reject these stations'
+ add_to_reject_list: [47095, 47098, 47101, 47102]
diff --git a/parm/jcb-gdas/observation_chronicle/snow/t06z/ghcn_snow.yaml b/parm/jcb-gdas/observation_chronicle/snow/t06z/ghcn_snow.yaml
new file mode 100644
index 000000000..20420eabd
--- /dev/null
+++ b/parm/jcb-gdas/observation_chronicle/snow/t06z/ghcn_snow.yaml
@@ -0,0 +1,14 @@
+# Instrument metadata
+# -------------------
+commissioned: 1900-01-01T00:00:00
+
+observer_type: conventional # Type of chronicle to use
+
+window_option: max
+
+# observation type initial configuration
+# --------------------------------
+stations_to_reject: [fakelist]
+
+# Chronicle of changes for this observation type
+# ----------------------------------------
diff --git a/parm/jcb-gdas/observation_chronicle/snow/t06z/madis_snow.yaml b/parm/jcb-gdas/observation_chronicle/snow/t06z/madis_snow.yaml
new file mode 100644
index 000000000..06a7560b2
--- /dev/null
+++ b/parm/jcb-gdas/observation_chronicle/snow/t06z/madis_snow.yaml
@@ -0,0 +1,15 @@
+# Instrument metadata
+# -------------------
+commissioned: 2021-01-01T06:00:00
+decommissioned: 2023-05-31T18:00:00
+
+observer_type: conventional # Type of chronicle to use
+
+window_option: max
+
+# observation type initial configuration
+# --------------------------------
+stations_to_reject: [BF001, BF002, BF004, BF009, BF010, BF012, BF017, BF019, BF030, BF034, BF035, BF036, BF037, BF038, BF044, BF049, BF052, BF054, BF056, BF059, BF061, BF066, BF069, BF078, BF080, BF084, BF086, BF089, BF091, BF110, BF117, BF121, BF122, BF123, BF132, BF137, BF142, BF143, BF150, BF151, BF159, BF191, BF197, BF209, BF215, BF233, BF234, BF235, BF242, BF284, BOWC1, BT007, BT008, BT116, BT117, BT119, BT128, BT140, CAAXM, CAINP, CALXV, CSNA2, FAFA2, HPN06, KESQ6, LACQ6, LPTUT, MKLA2, OHAW1, OJIM4, OKEQ6, SHDA2, TUNA2, UTRMD, WEAQ6, WINM4, XACC1]
+
+# Chronicle of changes for this observation type
+# ----------------------------------------
diff --git a/parm/jcb-gdas/observation_chronicle/snow/t06z/sfcsno.yaml b/parm/jcb-gdas/observation_chronicle/snow/t06z/sfcsno.yaml
new file mode 100644
index 000000000..4f4ff7be9
--- /dev/null
+++ b/parm/jcb-gdas/observation_chronicle/snow/t06z/sfcsno.yaml
@@ -0,0 +1,78 @@
+# Instrument metadata
+# -------------------
+commissioned: 1970-01-01T00:00:00
+
+observer_type: conventional # Type of chronicle to use
+
+window_option: max
+
+# observation type initial configuration
+# --------------------------------
+stations_to_reject: [71120, 71397, 71621, 71727, 71816 # from North America
+ , 71641, 71976, 71743, 71902
+ , 10863, 16179 # from Europe
+ , 40550, 40580, 40582, 40587, 40592 # Mid East
+ , 47005, 47008, 47014, 47016, 47020, 47022, 47025, 47028, 47031, 47035 # from North Korea
+ , 47037, 47039, 47041, 47046, 47050, 47052, 47055, 47058, 47060, 47061
+ , 47065, 47067, 47068, 47069, 47070, 47069, 47070, 47075, 47090
+ , 48698, 48830 # from Singapore
+ # Snow reports with frequent incorrect zero values in 06/12/18z cycles from China
+ , 50136, 50353, 50468, 50557, 50564, 50603, 50658, 50745, 50756, 50774 # from China
+ , 50788, 50844, 50854, 50888, 50949, 50953, 50963, 50968, 50978, 50983
+ , 51467, 51573, 51644, 51656, 51716, 51747, 51765, 51777, 51828, 51886
+ , 52203, 52267, 52323, 52418, 52436, 52533, 52652, 52681, 52713, 52754
+ , 52818, 52836, 52866, 52908, 52955, 52983, 53068, 53083, 53149, 53192
+ , 53231, 53276, 53336, 53352, 53391, 53463, 53480, 53487, 53502, 53513
+ , 53529, 53543, 53564, 53588, 53593, 53614, 53646, 53673, 53698, 53705
+ , 53723, 53764, 53772, 53787, 53798, 53845, 53863, 53898, 53915, 53923
+ , 53959, 53975, 54026, 54027, 54049, 54094, 54096, 54115, 54135, 54157
+ , 54161, 54186, 54208, 54218, 54226, 54236, 54259, 54273, 54292, 54308
+ , 54311, 54324, 54337, 54342, 54346, 54374, 54377, 54386, 54401, 54405
+ , 54423, 54436, 54471, 54493, 54497, 54511, 54527, 54534, 54539, 54602
+ , 54618, 54662, 54715, 54725, 54751, 54753, 54776, 54808, 54823, 54826
+ , 54836, 54843, 54857, 54863, 54909, 54916, 54929, 55279, 55472, 55578
+ , 55591, 55664, 55696, 55773, 56004, 56033, 56065, 56096, 56106, 56116
+ , 56137, 56146, 56172, 56182, 56257, 56357, 56374, 56586, 56691, 57014
+ , 57046, 57067, 57071, 57083, 57259, 57265, 57279, 57297, 57378, 57399
+ , 57461, 57476, 57494, 57554, 57584, 57655, 57707, 57712, 57731, 57745
+ , 57766, 57776, 57793, 57799, 57832, 57845, 57853, 57866, 57902, 57922
+ , 58027, 58141, 58150, 58208, 58265, 58345, 58437, 58477, 58506, 58543
+ , 58556, 58569, 58633, 58652, 58725, 58730, 58731, 58752
+ , 65250] # from Africa
+
+# Chronicle of changes for this observation type
+# ----------------------------------------
+chronicles:
+
+- action_date: "2021-10-01T00:00:00"
+ justification: 'These stations are okay from this time'
+ remove_from_reject_list: [71120, 71397, 71727, 71816]
+
+- action_date: "2022-10-01T00:00:00"
+ justification: 'These stations are okay from this time'
+ remove_from_reject_list: [50136
+ , 50353, 50468, 50557, 50564, 50603, 50658, 50745, 50756, 50774 # from China
+ , 50788, 50844, 50854, 50888, 50949, 50953, 50963, 50968, 50978, 50983
+ , 51467, 51573, 51644, 51656, 51716, 51747, 51765, 51777, 51828, 51886
+ , 52203, 52267, 52323, 52418, 52436, 52533, 52652, 52681, 52713, 52754
+ , 52818, 52836, 52866, 52908, 52955, 52983, 53068, 53083, 53149, 53192
+ , 53231, 53276, 53336, 53352, 53391, 53463, 53480, 53487, 53502, 53513
+ , 53529, 53543, 53564, 53588, 53593, 53614, 53646, 53673, 53698, 53705
+ , 53723, 53764, 53772, 53787, 53798, 53845, 53863, 53898, 53915, 53923
+ , 53959, 53975, 54026, 54027, 54049, 54094, 54096, 54115, 54135, 54157
+ , 54161, 54186, 54208, 54218, 54226, 54236, 54259, 54273, 54292, 54308
+ , 54311, 54324, 54337, 54342, 54346, 54374, 54377, 54386, 54401, 54405
+ , 54423, 54436, 54471, 54493, 54497, 54511, 54527, 54534, 54539, 54602
+ , 54618, 54662, 54715, 54725, 54751, 54753, 54776, 54808, 54823, 54826
+ , 54836, 54843, 54857, 54863, 54909, 54916, 54929, 55279, 55472, 55578
+ , 55591, 55664, 55696, 55773, 56004, 56033, 56065, 56096, 56106, 56116
+ , 56137, 56146, 56172, 56182, 56257, 56357, 56374, 56586, 56691, 57014
+ , 57046, 57067, 57071, 57083, 57259, 57265, 57279, 57297, 57378, 57399
+ , 57461, 57476, 57494, 57554, 57584, 57655, 57707, 57712, 57731, 57745
+ , 57766, 57776, 57793, 57799, 57832, 57845, 57853, 57866, 57902, 57922
+ , 58027, 58141, 58150, 58208, 58265, 58345, 58437, 58477, 58506, 58543
+ , 58556, 58569, 58633, 58652, 58725, 58730, 58731, 58752]
+
+- action_date: "2022-10-01T01:00:00"
+ justification: 'Add to reject these stations'
+ add_to_reject_list: [47095, 47098, 47101, 47102]
diff --git a/parm/jcb-gdas/observation_chronicle/snow/t06z/snocvr.yaml b/parm/jcb-gdas/observation_chronicle/snow/t06z/snocvr.yaml
new file mode 100644
index 000000000..0749e56ef
--- /dev/null
+++ b/parm/jcb-gdas/observation_chronicle/snow/t06z/snocvr.yaml
@@ -0,0 +1,14 @@
+# Instrument metadata
+# -------------------
+commissioned: 2023-05-01T00:00:00
+
+observer_type: conventional # Type of chronicle to use
+
+window_option: max
+
+# observation type initial configuration
+# --------------------------------
+stations_to_reject: [BFTU1, FRDN5, MWDO3, SGNN5, NUTA3, CNDA3, HBEA3, ELCN5]
+
+# Chronicle of changes for this observation type
+# ----------------------------------------
diff --git a/parm/jcb-gdas/observation_chronicle/snow/t06z/snocvr_snomad.yaml b/parm/jcb-gdas/observation_chronicle/snow/t06z/snocvr_snomad.yaml
new file mode 100644
index 000000000..41b3ed06c
--- /dev/null
+++ b/parm/jcb-gdas/observation_chronicle/snow/t06z/snocvr_snomad.yaml
@@ -0,0 +1,14 @@
+# Instrument metadata
+# -------------------
+commissioned: 2023-05-01T00:00:00
+
+observer_type: conventional # Type of chronicle to use
+
+window_option: max
+
+# observation type initial configuration
+# --------------------------------
+stations_to_reject: [fakelist]
+
+# Chronicle of changes for this observation type
+# ----------------------------------------
diff --git a/parm/jcb-gdas/observation_chronicle/snow/t06z/snomad.yaml b/parm/jcb-gdas/observation_chronicle/snow/t06z/snomad.yaml
new file mode 100644
index 000000000..9db6e445d
--- /dev/null
+++ b/parm/jcb-gdas/observation_chronicle/snow/t06z/snomad.yaml
@@ -0,0 +1,14 @@
+# Instrument metadata
+# -------------------
+commissioned: 2024-11-01T00:00:00
+
+observer_type: conventional # Type of chronicle to use
+
+window_option: max
+
+# observation type initial configuration
+# --------------------------------
+stations_to_reject: [fakelist]
+
+# Chronicle of changes for this observation type
+# ----------------------------------------
diff --git a/parm/jcb-gdas/observation_chronicle/snow/t12z b/parm/jcb-gdas/observation_chronicle/snow/t12z
new file mode 120000
index 000000000..e490a10cf
--- /dev/null
+++ b/parm/jcb-gdas/observation_chronicle/snow/t12z
@@ -0,0 +1 @@
+t06z
\ No newline at end of file
diff --git a/parm/jcb-gdas/observation_chronicle/snow/t18z b/parm/jcb-gdas/observation_chronicle/snow/t18z
new file mode 120000
index 000000000..e490a10cf
--- /dev/null
+++ b/parm/jcb-gdas/observation_chronicle/snow/t18z
@@ -0,0 +1 @@
+t06z
\ No newline at end of file
diff --git a/parm/jcb-gdas/observation_chronicle/soil/smap_soil.yaml b/parm/jcb-gdas/observation_chronicle/soil/smap_soil.yaml
new file mode 100644
index 000000000..af70c2a9d
--- /dev/null
+++ b/parm/jcb-gdas/observation_chronicle/soil/smap_soil.yaml
@@ -0,0 +1,14 @@
+# Instrument metadata
+# -------------------
+commissioned: 2015-01-31T00:00:00
+
+observer_type: conventional # Type of chronicle to use
+
+window_option: max
+
+# observation type initial configuration
+# --------------------------------
+stations_to_reject: [fakelist]
+
+# Chronicle of changes for this observation type
+# ----------------------------------------
diff --git a/parm/jcb-gdas/observation_statistics/aero/retrieval_aod_viirs_n20.yaml.j2 b/parm/jcb-gdas/observation_statistics/aero/retrieval_aod_viirs_n20.yaml.j2
new file mode 100644
index 000000000..efc7eeb68
--- /dev/null
+++ b/parm/jcb-gdas/observation_statistics/aero/retrieval_aod_viirs_n20.yaml.j2
@@ -0,0 +1,50 @@
+- obs space:
+ name: aod_n20
+ obsdatain:
+ engine:
+ type: H5File
+ obsfile: "{{ aero_obsdatain_path }}/{{ aero_obsdatain_prefix }}{{ observation_from_jcb }}{{ aero_obsdatain_suffix }}"
+ simulated variables: ['aerosolOpticalDepth']
+ observed variables: ['aerosolOpticalDepth']
+ variables: ['aerosolOpticalDepth']
+ groups to process: ['ombg', 'oman']
+ qc groups: ['EffectiveQC0', 'EffectiveQC1']
+ statistics to compute: ['mean', 'count', 'RMS']
+ output file: "{{ aero_obsdataout_path }}/{{ aero_obsdataout_prefix }}{{ observation_from_jcb }}{{ aero_obsdataout_suffix }}"
+ output ascii file: "{{ aero_obsdataout_path }}/{{ observation_from_jcb }}_ioda_stats.txt"
+ regular grid binning:
+ bin size in degrees: 5.0
+ use negative longitudes: true
+ domains to process:
+ - domain:
+ name: "SH"
+ first mask variable: latitude
+ first mask range: [-90,0]
+ - domain:
+ name: "NH"
+ first mask variable: latitude
+ first mask range: [0,90]
+ - domain:
+ name: "CONUS"
+ first mask variable: latitude
+ first mask range: [25,49]
+ second mask variable: longitude
+ second mask range: [-125,-66]
+ - domain:
+ name: "Europe"
+ first mask variable: latitude
+ first mask range: [35,70]
+ second mask variable: longitude
+ second mask range: [-11,38]
+ - domain:
+ name: "Africa"
+ first mask variable: latitude
+ first mask range: [-35,37]
+ second mask variable: longitude
+ second mask range: [-17,52]
+ - domain:
+ name: "Asia"
+ first mask variable: latitude
+ first mask range: [0,70]
+ second mask variable: longitude
+ second mask range: [38, 180]
diff --git a/parm/jcb-gdas/observation_statistics/aero/retrieval_aod_viirs_n21.yaml.j2 b/parm/jcb-gdas/observation_statistics/aero/retrieval_aod_viirs_n21.yaml.j2
new file mode 100644
index 000000000..b5ff3e457
--- /dev/null
+++ b/parm/jcb-gdas/observation_statistics/aero/retrieval_aod_viirs_n21.yaml.j2
@@ -0,0 +1,50 @@
+- obs space:
+ name: aod_n21
+ obsdatain:
+ engine:
+ type: H5File
+ obsfile: "{{ aero_obsdatain_path }}/{{ aero_obsdatain_prefix }}{{ observation_from_jcb }}{{ aero_obsdatain_suffix }}"
+ simulated variables: ['aerosolOpticalDepth']
+ observed variables: ['aerosolOpticalDepth']
+ variables: ['aerosolOpticalDepth']
+ groups to process: ['ombg', 'oman']
+ qc groups: ['EffectiveQC0', 'EffectiveQC1']
+ statistics to compute: ['mean', 'count', 'RMS']
+ output file: "{{ aero_obsdataout_path }}/{{ aero_obsdataout_prefix }}{{ observation_from_jcb }}{{ aero_obsdataout_suffix }}"
+ output ascii file: {{ aero_obsdataout_path }}/{{ observation_from_jcb }}_ioda_stats.txt
+ regular grid binning:
+ bin size in degrees: 5.0
+ use negative longitudes: true
+ domains to process:
+ - domain:
+ name: "SH"
+ first mask variable: latitude
+ first mask range: [-90,0]
+ - domain:
+ name: "NH"
+ first mask variable: latitude
+ first mask range: [0,90]
+ - domain:
+ name: "CONUS"
+ first mask variable: latitude
+ first mask range: [25,49]
+ second mask variable: longitude
+ second mask range: [-125,-66]
+ - domain:
+ name: "Europe"
+ first mask variable: latitude
+ first mask range: [35,70]
+ second mask variable: longitude
+ second mask range: [-11,38]
+ - domain:
+ name: "Africa"
+ first mask variable: latitude
+ first mask range: [-35,37]
+ second mask variable: longitude
+ second mask range: [-17,52]
+ - domain:
+ name: "Asia"
+ first mask variable: latitude
+ first mask range: [0,70]
+ second mask variable: longitude
+ second mask range: [38, 180]
diff --git a/parm/jcb-gdas/observation_statistics/aero/retrieval_aod_viirs_npp.yaml.j2 b/parm/jcb-gdas/observation_statistics/aero/retrieval_aod_viirs_npp.yaml.j2
new file mode 100644
index 000000000..ddbe9adcf
--- /dev/null
+++ b/parm/jcb-gdas/observation_statistics/aero/retrieval_aod_viirs_npp.yaml.j2
@@ -0,0 +1,50 @@
+- obs space:
+ name: aod_npp
+ obsdatain:
+ engine:
+ type: H5File
+ obsfile: "{{ aero_obsdatain_path }}/{{ aero_obsdatain_prefix }}{{ observation_from_jcb }}{{ aero_obsdatain_suffix }}"
+ simulated variables: ['aerosolOpticalDepth']
+ observed variables: ['aerosolOpticalDepth']
+ variables: ['aerosolOpticalDepth']
+ groups to process: ['ombg', 'oman']
+ qc groups: ['EffectiveQC0', 'EffectiveQC1']
+ statistics to compute: ['mean', 'count', 'RMS']
+ output file: "{{ aero_obsdataout_path }}/{{ aero_obsdataout_prefix }}{{ observation_from_jcb }}{{ aero_obsdataout_suffix }}"
+ output ascii file: "{{ aero_obsdataout_path }}/{{ observation_from_jcb }}_ioda_stats.txt"
+ regular grid binning:
+ bin size in degrees: 5.0
+ use negative longitudes: true
+ domains to process:
+ - domain:
+ name: "SH"
+ first mask variable: latitude
+ first mask range: [-90,0]
+ - domain:
+ name: "NH"
+ first mask variable: latitude
+ first mask range: [0,90]
+ - domain:
+ name: "CONUS"
+ first mask variable: latitude
+ first mask range: [25,49]
+ second mask variable: longitude
+ second mask range: [-125,-66]
+ - domain:
+ name: "Europe"
+ first mask variable: latitude
+ first mask range: [35,70]
+ second mask variable: longitude
+ second mask range: [-11,38]
+ - domain:
+ name: "Africa"
+ first mask variable: latitude
+ first mask range: [-35,37]
+ second mask variable: longitude
+ second mask range: [-17,52]
+ - domain:
+ name: "Asia"
+ first mask variable: latitude
+ first mask range: [0,70]
+ second mask variable: longitude
+ second mask range: [38, 180]
diff --git a/parm/jcb-gdas/observation_statistics/atmosphere/conventional_ps.yaml.j2 b/parm/jcb-gdas/observation_statistics/atmosphere/conventional_ps.yaml.j2
new file mode 100644
index 000000000..704072d5e
--- /dev/null
+++ b/parm/jcb-gdas/observation_statistics/atmosphere/conventional_ps.yaml.j2
@@ -0,0 +1,50 @@
+- obs space:
+ name: prepbufr_adpsfc
+ obsdatain:
+ engine:
+ type: H5File
+ obsfile: "{{ atmosphere_obsdatain_path }}/{{ atmosphere_obsdatain_prefix }}{{ observation_from_jcb }}{{ atmosphere_obsdatain_suffix }}"
+ simulated variables: ['stationPressure']
+ observed variables: ['stationPressure']
+ statistics to compute: ['mean', 'count', 'RMS']
+ variables: ['stationPressure']
+ groups to process: ['ombg', 'oman']
+ qc groups: ['EffectiveQC0', 'EffectiveQC1']
+ output file: "{{ atmosphere_obsdataout_path }}/{{ atmosphere_obsdataout_prefix }}{{ observation_from_jcb }}{{ atmosphere_obsdataout_suffix }}"
+ output ascii file: "{{ atmosphere_obsdataout_path }}/{{ observation_from_jcb }}_ioda_stats.txt"
+ regular grid binning:
+ bin size in degrees: 1.0
+ use negative longitudes: true
+ domains to process:
+ - domain:
+ name: "SH"
+ first mask variable: latitude
+ first mask range: [-90,0]
+ - domain:
+ name: "NH"
+ first mask variable: latitude
+ first mask range: [0,90]
+ - domain:
+ name: "CONUS"
+ first mask variable: latitude
+ first mask range: [25,49]
+ second mask variable: longitude
+ second mask range: [-125,-66]
+ - domain:
+ name: "Europe"
+ first mask variable: latitude
+ first mask range: [35,70]
+ second mask variable: longitude
+ second mask range: [-11,38]
+ - domain:
+ name: "Africa"
+ first mask variable: latitude
+ first mask range: [-35,37]
+ second mask variable: longitude
+ second mask range: [-17,52]
+ - domain:
+ name: "Asia"
+ first mask variable: latitude
+ first mask range: [0,70]
+ second mask variable: longitude
+ second mask range: [38, 180]
diff --git a/parm/jcb-gdas/observation_statistics/atmosphere/prepbufr_adpsfc.yaml.j2 b/parm/jcb-gdas/observation_statistics/atmosphere/prepbufr_adpsfc.yaml.j2
new file mode 100644
index 000000000..44cfcb445
--- /dev/null
+++ b/parm/jcb-gdas/observation_statistics/atmosphere/prepbufr_adpsfc.yaml.j2
@@ -0,0 +1,54 @@
+- obs space:
+ name: prepbufr_adpsfc
+ obsdatain:
+ engine:
+ type: H5File
+ obsfile: "{{ atmosphere_obsdatain_path }}/{{ atmosphere_obsdatain_prefix }}{{ observation_from_jcb }}{{ atmosphere_obsdatain_suffix }}"
+ simulated variables: ['stationPressure']
+ observed variables: ['stationPressure']
+ statistics to compute: ['mean', 'count', 'RMS']
+ variables: ['stationPressure']
+ groups to process: ['ombg', 'oman']
+ qc groups: ['EffectiveQC0', 'EffectiveQC1']
+ output file: "{{ atmosphere_obsdataout_path }}/{{ atmosphere_obsdataout_prefix }}{{ observation_from_jcb }}{{ atmosphere_obsdataout_suffix }}"
+ output ascii file: "{{ atmosphere_obsdataout_path }}/{{ observation_from_jcb }}_ioda_stats.txt"
+ ascii vertical bins:
+ vertical bin names: [1000+, 1000-900, 900-800, 800-600, 600-400, 400-300, 300-250, 250-200, 200-150, 150-100, 100-50]
+ vertical bin ranges: [100000, 90000, 80000, 60000, 40000, 30000, 25000, 20000, 15000, 10000, 5000]
+ vertical bin variable: pressure
+ regular grid binning:
+ bin size in degrees: 2.5
+ use negative longitudes: true
+ domains to process:
+ - domain:
+ name: "SH"
+ first mask variable: latitude
+ first mask range: [-90,0]
+ - domain:
+ name: "NH"
+ first mask variable: latitude
+ first mask range: [0,90]
+ - domain:
+ name: "CONUS"
+ first mask variable: latitude
+ first mask range: [25,49]
+ second mask variable: longitude
+ second mask range: [-125,-66]
+ - domain:
+ name: "Europe"
+ first mask variable: latitude
+ first mask range: [35,70]
+ second mask variable: longitude
+ second mask range: [-11,38]
+ - domain:
+ name: "Africa"
+ first mask variable: latitude
+ first mask range: [-35,37]
+ second mask variable: longitude
+ second mask range: [-17,52]
+ - domain:
+ name: "Asia"
+ first mask variable: latitude
+ first mask range: [0,70]
+ second mask variable: longitude
+ second mask range: [38, 180]
diff --git a/parm/jcb-gdas/observation_statistics/atmosphere/prepbufr_adpupa.yaml.j2 b/parm/jcb-gdas/observation_statistics/atmosphere/prepbufr_adpupa.yaml.j2
new file mode 100644
index 000000000..c732b701b
--- /dev/null
+++ b/parm/jcb-gdas/observation_statistics/atmosphere/prepbufr_adpupa.yaml.j2
@@ -0,0 +1,54 @@
+- obs space:
+ name: prepbufr_adpupa
+ obsdatain:
+ engine:
+ type: H5File
+ obsfile: "{{ atmosphere_obsdatain_path }}/{{ atmosphere_obsdatain_prefix }}{{ observation_from_jcb }}{{ atmosphere_obsdatain_suffix }}"
+ simulated variables: ['stationPressure']
+ observed variables: ['stationPressure']
+ statistics to compute: ['mean', 'count', 'RMS']
+ variables: ['stationPressure']
+ groups to process: ['ombg', 'oman']
+ qc groups: ['EffectiveQC0', 'EffectiveQC1']
+ output file: "{{ atmosphere_obsdataout_path }}/{{ atmosphere_obsdataout_prefix }}{{ observation_from_jcb }}{{ atmosphere_obsdataout_suffix }}"
+ output ascii file: "{{ atmosphere_obsdataout_path }}/{{ observation_from_jcb }}_ioda_stats.txt"
+ ascii vertical bins:
+ vertical bin names: [1000+, 1000-900, 900-800, 800-600, 600-400, 400-300, 300-250, 250-200, 200-150, 150-100, 100-50]
+ vertical bin ranges: [100000, 90000, 80000, 60000, 40000, 30000, 25000, 20000, 15000, 10000, 5000]
+ vertical bin variable: pressure
+ regular grid binning:
+ bin size in degrees: 2.5
+ use negative longitudes: true
+ domains to process:
+ - domain:
+ name: "SH"
+ first mask variable: latitude
+ first mask range: [-90,0]
+ - domain:
+ name: "NH"
+ first mask variable: latitude
+ first mask range: [0,90]
+ - domain:
+ name: "CONUS"
+ first mask variable: latitude
+ first mask range: [25,49]
+ second mask variable: longitude
+ second mask range: [-125,-66]
+ - domain:
+ name: "Europe"
+ first mask variable: latitude
+ first mask range: [35,70]
+ second mask variable: longitude
+ second mask range: [-11,38]
+ - domain:
+ name: "Africa"
+ first mask variable: latitude
+ first mask range: [-35,37]
+ second mask variable: longitude
+ second mask range: [-17,52]
+ - domain:
+ name: "Asia"
+ first mask variable: latitude
+ first mask range: [0,70]
+ second mask variable: longitude
+ second mask range: [38, 180]
diff --git a/parm/jcb-gdas/observation_statistics/atmosphere/prepbufr_sfcshp.yaml.j2 b/parm/jcb-gdas/observation_statistics/atmosphere/prepbufr_sfcshp.yaml.j2
new file mode 100644
index 000000000..9b24361c3
--- /dev/null
+++ b/parm/jcb-gdas/observation_statistics/atmosphere/prepbufr_sfcshp.yaml.j2
@@ -0,0 +1,54 @@
+- obs space:
+ name: prepbufr_sfcshp
+ obsdatain:
+ engine:
+ type: H5File
+ obsfile: "{{ atmosphere_obsdatain_path }}/{{ atmosphere_obsdatain_prefix }}{{ observation_from_jcb }}{{ atmosphere_obsdatain_suffix }}"
+ simulated variables: ['stationPressure']
+ observed variables: ['stationPressure']
+ statistics to compute: ['mean', 'count', 'RMS']
+ variables: ['stationPressure']
+ groups to process: ['ombg', 'oman']
+ qc groups: ['EffectiveQC0', 'EffectiveQC1']
+ output file: "{{ atmosphere_obsdataout_path }}/{{ atmosphere_obsdataout_prefix }}{{ observation_from_jcb }}{{ atmosphere_obsdataout_suffix }}"
+ output ascii file: "{{ atmosphere_obsdataout_path }}/{{ observation_from_jcb }}_ioda_stats.txt"
+ ascii vertical bins:
+ vertical bin names: [1000+, 1000-900, 900-800, 800-600, 600-400, 400-300, 300-250, 250-200, 200-150, 150-100, 100-50]
+ vertical bin ranges: [100000, 90000, 80000, 60000, 40000, 30000, 25000, 20000, 15000, 10000, 5000]
+ vertical bin variable: pressure
+ regular grid binning:
+ bin size in degrees: 2.5
+ use negative longitudes: true
+ domains to process:
+ - domain:
+ name: "SH"
+ first mask variable: latitude
+ first mask range: [-90,0]
+ - domain:
+ name: "NH"
+ first mask variable: latitude
+ first mask range: [0,90]
+ - domain:
+ name: "CONUS"
+ first mask variable: latitude
+ first mask range: [25,49]
+ second mask variable: longitude
+ second mask range: [-125,-66]
+ - domain:
+ name: "Europe"
+ first mask variable: latitude
+ first mask range: [35,70]
+ second mask variable: longitude
+ second mask range: [-11,38]
+ - domain:
+ name: "Africa"
+ first mask variable: latitude
+ first mask range: [-35,37]
+ second mask variable: longitude
+ second mask range: [-17,52]
+ - domain:
+ name: "Asia"
+ first mask variable: latitude
+ first mask range: [0,70]
+ second mask variable: longitude
+ second mask range: [38, 180]
diff --git a/parm/jcb-gdas/observation_statistics/atmosphere_gsi/aircraft_gsi.yaml.j2 b/parm/jcb-gdas/observation_statistics/atmosphere_gsi/aircraft_gsi.yaml.j2
new file mode 100644
index 000000000..9a1f3c802
--- /dev/null
+++ b/parm/jcb-gdas/observation_statistics/atmosphere_gsi/aircraft_gsi.yaml.j2
@@ -0,0 +1,54 @@
+- obs space:
+ name: aircraft_gsi
+ obsdatain:
+ engine:
+ type: H5File
+ obsfile: "{{ atmosphere_gsi_obsdatain_path }}/{{ atmosphere_gsi_obsdatain_prefix }}{{ observation_from_jcb }}{{ atmosphere_gsi_obsdatain_suffix }}"
+ simulated variables: ['airTemperature', 'specificHumidity', 'windEastward', 'windNorthward']
+ observed variables: ['airTemperature', 'specificHumidity', 'windEastward', 'windNorthward']
+ statistics to compute: ['mean', 'count', 'RMS']
+ variables: ['airTemperature', 'specificHumidity', 'windEastward', 'windNorthward']
+ groups to process: ['ombg', 'oman']
+ qc groups: ['GsiEffectiveQCGes', 'GsiEffectiveQCAnl']
+ output file: "{{ atmosphere_gsi_obsdataout_path }}/{{ atmosphere_gsi_obsdataout_prefix }}{{ observation_from_jcb }}{{ atmosphere_gsi_obsdataout_suffix }}"
+ output ascii file: "{{ atmosphere_gsi_obsdataout_path }}/{{ observation_from_jcb }}_ioda_stats.txt"
+ ascii vertical bins:
+ vertical bin names: [1000+, 1000-900, 900-800, 800-600, 600-400, 400-300, 300-250, 250-200, 200-150, 150-100, 100-50]
+ vertical bin ranges: [100000, 90000, 80000, 60000, 40000, 30000, 25000, 20000, 15000, 10000, 5000]
+ vertical bin variable: pressure
+ regular grid binning:
+ bin size in degrees: 2.5
+ use negative longitudes: true
+ domains to process:
+ - domain:
+ name: "SH"
+ first mask variable: latitude
+ first mask range: [-90,0]
+ - domain:
+ name: "NH"
+ first mask variable: latitude
+ first mask range: [0,90]
+ - domain:
+ name: "CONUS"
+ first mask variable: latitude
+ first mask range: [25,49]
+ second mask variable: longitude
+ second mask range: [-125,-66]
+ - domain:
+ name: "Europe"
+ first mask variable: latitude
+ first mask range: [35,70]
+ second mask variable: longitude
+ second mask range: [-11,38]
+ - domain:
+ name: "Africa"
+ first mask variable: latitude
+ first mask range: [-35,37]
+ second mask variable: longitude
+ second mask range: [-17,52]
+ - domain:
+ name: "Asia"
+ first mask variable: latitude
+ first mask range: [0,70]
+ second mask variable: longitude
+ second mask range: [38, 180]
diff --git a/parm/jcb-gdas/observation_statistics/atmosphere_gsi/atms_n20_gsi.yaml.j2 b/parm/jcb-gdas/observation_statistics/atmosphere_gsi/atms_n20_gsi.yaml.j2
new file mode 100644
index 000000000..067b7959a
--- /dev/null
+++ b/parm/jcb-gdas/observation_statistics/atmosphere_gsi/atms_n20_gsi.yaml.j2
@@ -0,0 +1,51 @@
+- obs space:
+ name: atms_n20_gsi
+ obsdatain:
+ engine:
+ type: H5File
+ obsfile: "{{ atmosphere_gsi_obsdatain_path }}/{{ atmosphere_gsi_obsdatain_prefix }}{{ observation_from_jcb }}{{ atmosphere_gsi_obsdatain_suffix }}"
+ simulated variables: ['brightnessTemperature']
+ observed variables: ['brightnessTemperature']
+ statistics to compute: ['count', 'mean', 'RMS']
+ variables: ['brightnessTemperature']
+ channels: [1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22]
+ groups to process: ['ombg', 'oman']
+ qc groups: ['GsiEffectiveQCGes', 'GsiEffectiveQCAnl']
+ output file: "{{ atmosphere_gsi_obsdataout_path }}/{{ atmosphere_gsi_obsdataout_prefix }}{{ observation_from_jcb }}{{ atmosphere_gsi_obsdataout_suffix }}"
+ output ascii file: "{{ atmosphere_gsi_obsdataout_path }}/{{ observation_from_jcb }}_ioda_stats.txt"
+ regular grid binning:
+ bin size in degrees: 2.5
+ use negative longitudes: true
+ domains to process:
+ - domain:
+ name: "SH"
+ first mask variable: latitude
+ first mask range: [-90,0]
+ - domain:
+ name: "NH"
+ first mask variable: latitude
+ first mask range: [0,90]
+ - domain:
+ name: "CONUS"
+ first mask variable: latitude
+ first mask range: [25,49]
+ second mask variable: longitude
+ second mask range: [-125,-66]
+ - domain:
+ name: "Europe"
+ first mask variable: latitude
+ first mask range: [35,70]
+ second mask variable: longitude
+ second mask range: [-11,38]
+ - domain:
+ name: "Africa"
+ first mask variable: latitude
+ first mask range: [-35,37]
+ second mask variable: longitude
+ second mask range: [-17,52]
+ - domain:
+ name: "Asia"
+ first mask variable: latitude
+ first mask range: [0,70]
+ second mask variable: longitude
+ second mask range: [38, 180]
diff --git a/parm/jcb-gdas/observation_statistics/atmosphere_gsi/sfc_gsi.yaml.j2 b/parm/jcb-gdas/observation_statistics/atmosphere_gsi/sfc_gsi.yaml.j2
new file mode 100644
index 000000000..2f6f5b7c4
--- /dev/null
+++ b/parm/jcb-gdas/observation_statistics/atmosphere_gsi/sfc_gsi.yaml.j2
@@ -0,0 +1,54 @@
+- obs space:
+ name: sfc_gsi
+ obsdatain:
+ engine:
+ type: H5File
+ obsfile: "{{ atmosphere_gsi_obsdatain_path }}/{{ atmosphere_gsi_obsdatain_prefix }}{{ observation_from_jcb }}{{ atmosphere_gsi_obsdatain_suffix }}"
+ simulated variables: ['stationPressure', 'airTemperature', 'specificHumidity', 'windEastward', 'windNorthward']
+ observed variables: ['stationPressure', 'airTemperature', 'specificHumidity', 'windEastward', 'windNorthward']
+ statistics to compute: ['mean', 'count', 'RMS']
+ variables: ['stationPressure', 'airTemperature', 'specificHumidity', 'windEastward', 'windNorthward']
+ groups to process: ['ombg', 'oman']
+ qc groups: ['GsiEffectiveQCGes', 'GsiEffectiveQCAnl']
+ output file: "{{ atmosphere_gsi_obsdataout_path }}/{{ atmosphere_gsi_obsdataout_prefix }}{{ observation_from_jcb }}{{ atmosphere_gsi_obsdataout_suffix }}"
+ output ascii file: "{{ atmosphere_gsi_obsdataout_path }}/{{ observation_from_jcb }}_ioda_stats.txt"
+ ascii vertical bins:
+ vertical bin names: [1000+, 1000-900, 900-800, 800-600, 600-400, 400-300, 300-250, 250-200, 200-150, 150-100, 100-50]
+ vertical bin ranges: [100000, 90000, 80000, 60000, 40000, 30000, 25000, 20000, 15000, 10000, 5000]
+ vertical bin variable: pressure
+ regular grid binning:
+ bin size in degrees: 2.5
+ use negative longitudes: true
+ domains to process:
+ - domain:
+ name: "SH"
+ first mask variable: latitude
+ first mask range: [-90,0]
+ - domain:
+ name: "NH"
+ first mask variable: latitude
+ first mask range: [0,90]
+ - domain:
+ name: "CONUS"
+ first mask variable: latitude
+ first mask range: [25,49]
+ second mask variable: longitude
+ second mask range: [-125,-66]
+ - domain:
+ name: "Europe"
+ first mask variable: latitude
+ first mask range: [35,70]
+ second mask variable: longitude
+ second mask range: [-11,38]
+ - domain:
+ name: "Africa"
+ first mask variable: latitude
+ first mask range: [-35,37]
+ second mask variable: longitude
+ second mask range: [-17,52]
+ - domain:
+ name: "Asia"
+ first mask variable: latitude
+ first mask range: [0,70]
+ second mask variable: longitude
+ second mask range: [38, 180]
diff --git a/parm/jcb-gdas/observation_statistics/atmosphere_gsi/sfcship_gsi.yaml.j2 b/parm/jcb-gdas/observation_statistics/atmosphere_gsi/sfcship_gsi.yaml.j2
new file mode 100644
index 000000000..5341825be
--- /dev/null
+++ b/parm/jcb-gdas/observation_statistics/atmosphere_gsi/sfcship_gsi.yaml.j2
@@ -0,0 +1,54 @@
+- obs space:
+ name: sfcship_gsi
+ obsdatain:
+ engine:
+ type: H5File
+ obsfile: "{{ atmosphere_gsi_obsdatain_path }}/{{ atmosphere_gsi_obsdatain_prefix }}{{ observation_from_jcb }}{{ atmosphere_gsi_obsdatain_suffix }}"
+ simulated variables: ['stationPressure', 'airTemperature', 'virtualTemperature', 'specificHumidity', 'windEastward', 'windNorthward']
+ observed variables: ['stationPressure', 'airTemperature', 'virtualTemperature', 'specificHumidity', 'windEastward', 'windNorthward']
+ statistics to compute: ['mean', 'count', 'RMS']
+ variables: ['stationPressure', 'airTemperature', 'virtualTemperature', 'specificHumidity', 'windEastward', 'windNorthward']
+ groups to process: ['ombg', 'oman']
+ qc groups: ['GsiEffectiveQCGes', 'GsiEffectiveQCAnl']
+ output file: "{{ atmosphere_gsi_obsdataout_path }}/{{ atmosphere_gsi_obsdataout_prefix }}{{ observation_from_jcb }}{{ atmosphere_gsi_obsdataout_suffix }}"
+ output ascii file: "{{ atmosphere_gsi_obsdataout_path }}/{{ observation_from_jcb }}_ioda_stats.txt"
+ ascii vertical bins:
+ vertical bin names: [1000+, 1000-900, 900-800, 800-600, 600-400, 400-300, 300-250, 250-200, 200-150, 150-100, 100-50]
+ vertical bin ranges: [100000, 90000, 80000, 60000, 40000, 30000, 25000, 20000, 15000, 10000, 5000]
+ vertical bin variable: pressure
+ regular grid binning:
+ bin size in degrees: 2.5
+ use negative longitudes: true
+ domains to process:
+ - domain:
+ name: "SH"
+ first mask variable: latitude
+ first mask range: [-90,0]
+ - domain:
+ name: "NH"
+ first mask variable: latitude
+ first mask range: [0,90]
+ - domain:
+ name: "CONUS"
+ first mask variable: latitude
+ first mask range: [25,49]
+ second mask variable: longitude
+ second mask range: [-125,-66]
+ - domain:
+ name: "Europe"
+ first mask variable: latitude
+ first mask range: [35,70]
+ second mask variable: longitude
+ second mask range: [-11,38]
+ - domain:
+ name: "Africa"
+ first mask variable: latitude
+ first mask range: [-35,37]
+ second mask variable: longitude
+ second mask range: [-17,52]
+ - domain:
+ name: "Asia"
+ first mask variable: latitude
+ first mask range: [0,70]
+ second mask variable: longitude
+ second mask range: [38, 180]
diff --git a/parm/jcb-gdas/observation_statistics/atmosphere_gsi/sondes_gsi.yaml.j2 b/parm/jcb-gdas/observation_statistics/atmosphere_gsi/sondes_gsi.yaml.j2
new file mode 100644
index 000000000..533dab478
--- /dev/null
+++ b/parm/jcb-gdas/observation_statistics/atmosphere_gsi/sondes_gsi.yaml.j2
@@ -0,0 +1,54 @@
+- obs space:
+ name: sondes_gsi
+ obsdatain:
+ engine:
+ type: H5File
+ obsfile: "{{ atmosphere_gsi_obsdatain_path }}/{{ atmosphere_gsi_obsdatain_prefix }}{{ observation_from_jcb }}{{ atmosphere_gsi_obsdatain_suffix }}"
+ simulated variables: ['stationPressure', 'airTemperature', 'virtualTemperature', 'specificHumidity', 'windEastward', 'windNorthward']
+ observed variables: ['stationPressure', 'airTemperature', 'virtualTemperature', 'specificHumidity', 'windEastward', 'windNorthward']
+ statistics to compute: ['mean', 'count', 'RMS']
+ variables: ['stationPressure', 'airTemperature', 'virtualTemperature', 'specificHumidity', 'windEastward', 'windNorthward']
+ groups to process: ['ombg', 'oman']
+ qc groups: ['GsiEffectiveQCGes', 'GsiEffectiveQCAnl']
+ output file: "{{ atmosphere_gsi_obsdataout_path }}/{{ atmosphere_gsi_obsdataout_prefix }}{{ observation_from_jcb }}{{ atmosphere_gsi_obsdataout_suffix }}"
+ output ascii file: "{{ atmosphere_gsi_obsdataout_path }}/{{ observation_from_jcb }}_ioda_stats.txt"
+ ascii vertical bins:
+ vertical bin names: [1000+, 1000-900, 900-800, 800-600, 600-400, 400-300, 300-250, 250-200, 200-150, 150-100, 100-50]
+ vertical bin ranges: [100000, 90000, 80000, 60000, 40000, 30000, 25000, 20000, 15000, 10000, 5000]
+ vertical bin variable: pressure
+ regular grid binning:
+ bin size in degrees: 2.5
+ use negative longitudes: true
+ domains to process:
+ - domain:
+ name: "SH"
+ first mask variable: latitude
+ first mask range: [-90,0]
+ - domain:
+ name: "NH"
+ first mask variable: latitude
+ first mask range: [0,90]
+ - domain:
+ name: "CONUS"
+ first mask variable: latitude
+ first mask range: [25,49]
+ second mask variable: longitude
+ second mask range: [-125,-66]
+ - domain:
+ name: "Europe"
+ first mask variable: latitude
+ first mask range: [35,70]
+ second mask variable: longitude
+ second mask range: [-11,38]
+ - domain:
+ name: "Africa"
+ first mask variable: latitude
+ first mask range: [-35,37]
+ second mask variable: longitude
+ second mask range: [-17,52]
+ - domain:
+ name: "Asia"
+ first mask variable: latitude
+ first mask range: [0,70]
+ second mask variable: longitude
+ second mask range: [38, 180]
diff --git a/parm/jcb-gdas/observation_statistics/snow/ims_snow.yaml.j2 b/parm/jcb-gdas/observation_statistics/snow/ims_snow.yaml.j2
new file mode 100644
index 000000000..7f584d785
--- /dev/null
+++ b/parm/jcb-gdas/observation_statistics/snow/ims_snow.yaml.j2
@@ -0,0 +1,69 @@
+- obs space:
+ name: ims_snow
+ obsdatain:
+ engine:
+ type: H5File
+ obsfile: "{{ snow_obsdatain_path }}/{{ snow_obsdatain_prefix }}{{ observation_from_jcb }}{{ snow_obsdatain_suffix }}"
+ simulated variables: ['totalSnowDepth']
+ observed variables: ['totalSnowDepth']
+ statistics to compute: ['mean', 'count', 'RMS']
+ variables: [totalSnowDepth]
+ groups to process: ['ombg', 'oman']
+ qc groups: ['EffectiveQC0', 'EffectiveQC1']
+ output file: "{{ snow_obsdataout_path }}/{{ snow_obsdataout_prefix }}{{ observation_from_jcb }}{{ snow_obsdataout_suffix }}"
+ output ascii file: "{{ snow_obsdataout_path }}/{{ observation_from_jcb }}_ioda_stats.txt"
+ regular grid binning:
+ bin size in degrees: 2.0
+ use negative longitudes: false
+ domains to process:
+ - domain:
+ name: "SH"
+ first mask variable: latitude
+ first mask range: [-90,0]
+ - domain:
+ name: "NH"
+ first mask variable: latitude
+ first mask range: [0,90]
+ - domain:
+ name: "West_CONUS"
+ first mask variable: latitude
+ first mask range: [25,49]
+ second mask variable: longitude
+ second mask range: [235,260]
+ - domain:
+ name: "East_CONUS"
+ first mask variable: latitude
+ first mask range: [25,49]
+ second mask variable: longitude
+ second mask range: [260,294]
+ - domain:
+ name: "Alaska"
+ first mask variable: latitude
+ first mask range: [52,72]
+ second mask variable: longitude
+ second mask range: [190,230]
+ - domain:
+ name: "Europe"
+ first mask variable: latitude
+ first mask range: [35,70]
+ second mask variable: longitude
+ second mask range: [38,349]
+ - domain:
+ name: "Africa"
+ first mask variable: latitude
+ first mask range: [-35,37]
+ second mask variable: longitude
+ second mask range: [52,343]
+ - domain:
+ name: "Asia"
+ first mask variable: latitude
+ first mask range: [0,70]
+ second mask variable: longitude
+ second mask range: [38, 180]
+ - domain:
+ name: "High_Mount_Asia"
+ first mask variable: latitude
+ first mask range: [20,46]
+ second mask variable: longitude
+ second mask range: [60, 111]
+
diff --git a/parm/jcb-gdas/observation_statistics/snow/madis_snow.yaml.j2 b/parm/jcb-gdas/observation_statistics/snow/madis_snow.yaml.j2
new file mode 100644
index 000000000..63fd6678b
--- /dev/null
+++ b/parm/jcb-gdas/observation_statistics/snow/madis_snow.yaml.j2
@@ -0,0 +1,69 @@
+- obs space:
+ name: madis_snow
+ obsdatain:
+ engine:
+ type: H5File
+ obsfile: "{{ snow_obsdatain_path }}/{{ snow_obsdatain_prefix }}{{ observation_from_jcb }}{{ snow_obsdatain_suffix }}"
+ simulated variables: ['totalSnowDepth']
+ observed variables: ['totalSnowDepth']
+ statistics to compute: ['mean', 'count', 'RMS']
+ variables: [totalSnowDepth]
+ groups to process: ['ombg', 'oman']
+ qc groups: ['EffectiveQC0', 'EffectiveQC1']
+ output file: "{{ snow_obsdataout_path }}/{{ snow_obsdataout_prefix }}{{ observation_from_jcb }}{{ snow_obsdataout_suffix }}"
+ output ascii file: "{{ snow_obsdataout_path }}/{{ observation_from_jcb }}_ioda_stats.txt"
+ regular grid binning:
+ bin size in degrees: 1.0
+ use negative longitudes: true
+ domains to process:
+ - domain:
+ name: "SH"
+ first mask variable: latitude
+ first mask range: [-90,0]
+ - domain:
+ name: "NH"
+ first mask variable: latitude
+ first mask range: [0,90]
+ - domain:
+ name: "West_CONUS"
+ first mask variable: latitude
+ first mask range: [25,49]
+ second mask variable: longitude
+ second mask range: [-125,-100]
+ - domain:
+ name: "East_CONUS"
+ first mask variable: latitude
+ first mask range: [25,49]
+ second mask variable: longitude
+ second mask range: [-100,-66]
+ - domain:
+ name: "Alaska"
+ first mask variable: latitude
+ first mask range: [52,72]
+ second mask variable: longitude
+ second mask range: [-170,-130]
+ - domain:
+ name: "Europe"
+ first mask variable: latitude
+ first mask range: [35,70]
+ second mask variable: longitude
+ second mask range: [-11,38]
+ - domain:
+ name: "Africa"
+ first mask variable: latitude
+ first mask range: [-35,37]
+ second mask variable: longitude
+ second mask range: [-17,52]
+ - domain:
+ name: "Asia"
+ first mask variable: latitude
+ first mask range: [0,70]
+ second mask variable: longitude
+ second mask range: [38, 180]
+ - domain:
+ name: "High_Mount_Asia"
+ first mask variable: latitude
+ first mask range: [20,46]
+ second mask variable: longitude
+ second mask range: [60, 111]
+
diff --git a/parm/jcb-gdas/observation_statistics/snow/sfcsno.yaml.j2 b/parm/jcb-gdas/observation_statistics/snow/sfcsno.yaml.j2
new file mode 100644
index 000000000..818a23065
--- /dev/null
+++ b/parm/jcb-gdas/observation_statistics/snow/sfcsno.yaml.j2
@@ -0,0 +1,69 @@
+- obs space:
+ name: sfcsno
+ obsdatain:
+ engine:
+ type: H5File
+ obsfile: "{{ snow_obsdatain_path }}/{{ snow_obsdatain_prefix }}{{ observation_from_jcb }}{{ snow_obsdatain_suffix }}"
+ simulated variables: ['totalSnowDepth']
+ observed variables: ['totalSnowDepth']
+ statistics to compute: ['mean', 'count', 'RMS']
+ variables: [totalSnowDepth]
+ groups to process: ['ombg', 'oman']
+ qc groups: ['EffectiveQC0', 'EffectiveQC1']
+ output file: "{{ snow_obsdataout_path }}/{{ snow_obsdataout_prefix }}{{ observation_from_jcb }}{{ snow_obsdataout_suffix }}"
+ output ascii file: "{{ snow_obsdataout_path }}/{{ observation_from_jcb }}_ioda_stats.txt"
+ regular grid binning:
+ bin size in degrees: 1.0
+ use negative longitudes: true
+ domains to process:
+ - domain:
+ name: "SH"
+ first mask variable: latitude
+ first mask range: [-90,0]
+ - domain:
+ name: "NH"
+ first mask variable: latitude
+ first mask range: [0,90]
+ - domain:
+ name: "West_CONUS"
+ first mask variable: latitude
+ first mask range: [25,49]
+ second mask variable: longitude
+ second mask range: [-125,-100]
+ - domain:
+ name: "East_CONUS"
+ first mask variable: latitude
+ first mask range: [25,49]
+ second mask variable: longitude
+ second mask range: [-100,-66]
+ - domain:
+ name: "Alaska"
+ first mask variable: latitude
+ first mask range: [52,72]
+ second mask variable: longitude
+ second mask range: [-170,-130]
+ - domain:
+ name: "Europe"
+ first mask variable: latitude
+ first mask range: [35,70]
+ second mask variable: longitude
+ second mask range: [-11,38]
+ - domain:
+ name: "Africa"
+ first mask variable: latitude
+ first mask range: [-35,37]
+ second mask variable: longitude
+ second mask range: [-17,52]
+ - domain:
+ name: "Asia"
+ first mask variable: latitude
+ first mask range: [0,70]
+ second mask variable: longitude
+ second mask range: [38, 180]
+ - domain:
+ name: "High_Mount_Asia"
+ first mask variable: latitude
+ first mask range: [20,46]
+ second mask variable: longitude
+ second mask range: [60, 111]
+
diff --git a/parm/jcb-gdas/observation_statistics/snow/snocvr.yaml.j2 b/parm/jcb-gdas/observation_statistics/snow/snocvr.yaml.j2
new file mode 100644
index 000000000..d90590f82
--- /dev/null
+++ b/parm/jcb-gdas/observation_statistics/snow/snocvr.yaml.j2
@@ -0,0 +1,69 @@
+- obs space:
+ name: snocvr
+ obsdatain:
+ engine:
+ type: H5File
+ obsfile: "{{ snow_obsdatain_path }}/{{ snow_obsdatain_prefix }}{{ observation_from_jcb }}{{ snow_obsdatain_suffix }}"
+ simulated variables: ['totalSnowDepth']
+ observed variables: ['totalSnowDepth']
+ statistics to compute: ['mean', 'count', 'RMS']
+ variables: [totalSnowDepth]
+ groups to process: ['ombg', 'oman']
+ qc groups: ['EffectiveQC0', 'EffectiveQC1']
+ output file: "{{ snow_obsdataout_path }}/{{ snow_obsdataout_prefix }}{{ observation_from_jcb }}{{ snow_obsdataout_suffix }}"
+ output ascii file: "{{ snow_obsdataout_path }}/{{ observation_from_jcb }}_ioda_stats.txt"
+ regular grid binning:
+ bin size in degrees: 1.0
+ use negative longitudes: true
+ domains to process:
+ - domain:
+ name: "SH"
+ first mask variable: latitude
+ first mask range: [-90,0]
+ - domain:
+ name: "NH"
+ first mask variable: latitude
+ first mask range: [0,90]
+ - domain:
+ name: "West_CONUS"
+ first mask variable: latitude
+ first mask range: [25,49]
+ second mask variable: longitude
+ second mask range: [-125,-100]
+ - domain:
+ name: "East_CONUS"
+ first mask variable: latitude
+ first mask range: [25,49]
+ second mask variable: longitude
+ second mask range: [-100,-66]
+ - domain:
+ name: "Alaska"
+ first mask variable: latitude
+ first mask range: [52,72]
+ second mask variable: longitude
+ second mask range: [-170,-130]
+ - domain:
+ name: "Europe"
+ first mask variable: latitude
+ first mask range: [35,70]
+ second mask variable: longitude
+ second mask range: [-11,38]
+ - domain:
+ name: "Africa"
+ first mask variable: latitude
+ first mask range: [-35,37]
+ second mask variable: longitude
+ second mask range: [-17,52]
+ - domain:
+ name: "Asia"
+ first mask variable: latitude
+ first mask range: [0,70]
+ second mask variable: longitude
+ second mask range: [38, 180]
+ - domain:
+ name: "High_Mount_Asia"
+ first mask variable: latitude
+ first mask range: [20,46]
+ second mask variable: longitude
+ second mask range: [60, 111]
+
diff --git a/parm/jcb-gdas/observation_statistics/snow/snocvr_snomad.yaml.j2 b/parm/jcb-gdas/observation_statistics/snow/snocvr_snomad.yaml.j2
new file mode 100644
index 000000000..f175d6e21
--- /dev/null
+++ b/parm/jcb-gdas/observation_statistics/snow/snocvr_snomad.yaml.j2
@@ -0,0 +1,69 @@
+- obs space:
+ name: snocvr_snomad
+ obsdatain:
+ engine:
+ type: H5File
+ obsfile: "{{ snow_obsdatain_path }}/{{ snow_obsdatain_prefix }}{{ observation_from_jcb }}{{ snow_obsdatain_suffix }}"
+ simulated variables: ['totalSnowDepth']
+ observed variables: ['totalSnowDepth']
+ statistics to compute: ['mean', 'count', 'RMS']
+ variables: [totalSnowDepth]
+ groups to process: ['ombg', 'oman']
+ qc groups: ['EffectiveQC0', 'EffectiveQC1']
+ output file: "{{ snow_obsdataout_path }}/{{ snow_obsdataout_prefix }}{{ observation_from_jcb }}{{ snow_obsdataout_suffix }}"
+ output ascii file: "{{ snow_obsdataout_path }}/{{ observation_from_jcb }}_ioda_stats.txt"
+ regular grid binning:
+ bin size in degrees: 1.0
+ use negative longitudes: true
+ domains to process:
+ - domain:
+ name: "SH"
+ first mask variable: latitude
+ first mask range: [-90,0]
+ - domain:
+ name: "NH"
+ first mask variable: latitude
+ first mask range: [0,90]
+ - domain:
+ name: "West_CONUS"
+ first mask variable: latitude
+ first mask range: [25,49]
+ second mask variable: longitude
+ second mask range: [-125,-100]
+ - domain:
+ name: "East_CONUS"
+ first mask variable: latitude
+ first mask range: [25,49]
+ second mask variable: longitude
+ second mask range: [-100,-66]
+ - domain:
+ name: "Alaska"
+ first mask variable: latitude
+ first mask range: [52,72]
+ second mask variable: longitude
+ second mask range: [-170,-130]
+ - domain:
+ name: "Europe"
+ first mask variable: latitude
+ first mask range: [35,70]
+ second mask variable: longitude
+ second mask range: [-11,38]
+ - domain:
+ name: "Africa"
+ first mask variable: latitude
+ first mask range: [-35,37]
+ second mask variable: longitude
+ second mask range: [-17,52]
+ - domain:
+ name: "Asia"
+ first mask variable: latitude
+ first mask range: [0,70]
+ second mask variable: longitude
+ second mask range: [38, 180]
+ - domain:
+ name: "High_Mount_Asia"
+ first mask variable: latitude
+ first mask range: [20,46]
+ second mask variable: longitude
+ second mask range: [60, 111]
+
diff --git a/parm/jcb-gdas/observation_statistics/snow/snomad.yaml.j2 b/parm/jcb-gdas/observation_statistics/snow/snomad.yaml.j2
new file mode 100644
index 000000000..1bdde113d
--- /dev/null
+++ b/parm/jcb-gdas/observation_statistics/snow/snomad.yaml.j2
@@ -0,0 +1,69 @@
+- obs space:
+ name: snomad
+ obsdatain:
+ engine:
+ type: H5File
+ obsfile: "{{ snow_obsdatain_path }}/{{ snow_obsdatain_prefix }}{{ observation_from_jcb }}{{ snow_obsdatain_suffix }}"
+ simulated variables: ['totalSnowDepth']
+ observed variables: ['totalSnowDepth']
+ statistics to compute: ['mean', 'count', 'RMS']
+ variables: [totalSnowDepth]
+ groups to process: ['ombg', 'oman']
+ qc groups: ['EffectiveQC0', 'EffectiveQC1']
+ output file: "{{ snow_obsdataout_path }}/{{ snow_obsdataout_prefix }}{{ observation_from_jcb }}{{ snow_obsdataout_suffix }}"
+ output ascii file: "{{ snow_obsdataout_path }}/{{ observation_from_jcb }}_ioda_stats.txt"
+ regular grid binning:
+ bin size in degrees: 1.0
+ use negative longitudes: true
+ domains to process:
+ - domain:
+ name: "SH"
+ first mask variable: latitude
+ first mask range: [-90,0]
+ - domain:
+ name: "NH"
+ first mask variable: latitude
+ first mask range: [0,90]
+ - domain:
+ name: "West_CONUS"
+ first mask variable: latitude
+ first mask range: [25,49]
+ second mask variable: longitude
+ second mask range: [-125,-100]
+ - domain:
+ name: "East_CONUS"
+ first mask variable: latitude
+ first mask range: [25,49]
+ second mask variable: longitude
+ second mask range: [-100,-66]
+ - domain:
+ name: "Alaska"
+ first mask variable: latitude
+ first mask range: [52,72]
+ second mask variable: longitude
+ second mask range: [-170,-130]
+ - domain:
+ name: "Europe"
+ first mask variable: latitude
+ first mask range: [35,70]
+ second mask variable: longitude
+ second mask range: [-11,38]
+ - domain:
+ name: "Africa"
+ first mask variable: latitude
+ first mask range: [-35,37]
+ second mask variable: longitude
+ second mask range: [-17,52]
+ - domain:
+ name: "Asia"
+ first mask variable: latitude
+ first mask range: [0,70]
+ second mask variable: longitude
+ second mask range: [38, 180]
+ - domain:
+ name: "High_Mount_Asia"
+ first mask variable: latitude
+ first mask range: [20,46]
+ second mask variable: longitude
+ second mask range: [60, 111]
+
diff --git a/parm/jcb-gdas/observations/aero/retrieval_aod_viirs_n20.yaml.j2 b/parm/jcb-gdas/observations/aero/retrieval_aod_viirs_n20.yaml.j2
new file mode 100644
index 000000000..378358946
--- /dev/null
+++ b/parm/jcb-gdas/observations/aero/retrieval_aod_viirs_n20.yaml.j2
@@ -0,0 +1,64 @@
+-
+
+ # Observation Space (I/O)
+ # -----------------------
+ obs space:
+ name: {{observation_from_jcb}}
+ obsdatain:
+ engine:
+ type: H5File
+ obsfile: "{{aero_obsdatain_path}}/{{aero_obsdatain_prefix}}{{observation_from_jcb}}{{aero_obsdatain_suffix}}"
+ missing file action: warn
+ obsdataout:
+ engine:
+ type: H5File
+ obsfile: "{{aero_obsdataout_path}}/{{aero_obsdataout_prefix}}{{observation_from_jcb}}{{aero_obsdataout_suffix}}"
+ io pool:
+ max pool size: 2
+ simulated variables: [aerosolOpticalDepth]
+ channels: 4
+
+ # Observation Operator
+ # --------------------
+ get values:
+ interpolation method: barycentric
+ time interpolation: linear
+ obs operator:
+ name: AodCRTM
+ Absorbers: [H2O,O3]
+ obs options:
+ Sensor_ID: &{{observation_from_jcb}}_sensor_id v.viirs-m_j1
+ EndianType: little_endian
+ AerosolOption: aerosols_gocart_default
+ CoefficientPath: "{{crtm_coefficient_path}}"
+ obs error:
+ covariance model: diagonal
+
+ # Observation Bias Correction (VarBC)
+ # -----------------------------------
+
+ # Observation Filters (QC)
+ # ------------------------
+ obs filters:
+ - filter: PreQC
+ maxvalue: 1
+ - filter: Domain Check
+ where:
+ - variable:
+ name: latitude@MetaData
+ minvalue: -60
+ maxvalue: 60
+ - filter: Bounds Check
+ filter variables:
+ - name: aerosolOpticalDepth
+ channels: 4
+ minvalue: 0
+ maxvalue: 4.9
+ action:
+ name: reject
+ - filter: Background Check
+ channels: 4
+ threshold: 3.0
+ action:
+ name: inflate error
+ inflation factor: 3.0
diff --git a/parm/jcb-gdas/observations/aero/retrieval_aod_viirs_n21.yaml.j2 b/parm/jcb-gdas/observations/aero/retrieval_aod_viirs_n21.yaml.j2
new file mode 100644
index 000000000..efa9cdd5c
--- /dev/null
+++ b/parm/jcb-gdas/observations/aero/retrieval_aod_viirs_n21.yaml.j2
@@ -0,0 +1,64 @@
+-
+
+ # Observation Space (I/O)
+ # -----------------------
+ obs space:
+ name: {{observation_from_jcb}}
+ obsdatain:
+ engine:
+ type: H5File
+ obsfile: "{{aero_obsdatain_path}}/{{aero_obsdatain_prefix}}{{observation_from_jcb}}{{aero_obsdatain_suffix}}"
+ missing file action: warn
+ obsdataout:
+ engine:
+ type: H5File
+ obsfile: "{{aero_obsdataout_path}}/{{aero_obsdataout_prefix}}{{observation_from_jcb}}{{aero_obsdataout_suffix}}"
+ io pool:
+ max pool size: 2
+ simulated variables: [aerosolOpticalDepth]
+ channels: 4
+
+ # Observation Operator
+ # --------------------
+ get values:
+ interpolation method: barycentric
+ time interpolation: linear
+ obs operator:
+ name: AodCRTM
+ Absorbers: [H2O,O3]
+ obs options:
+ Sensor_ID: &{{observation_from_jcb}}_sensor_id v.viirs-m_j2
+ EndianType: little_endian
+ AerosolOption: aerosols_gocart_default
+ CoefficientPath: "{{crtm_coefficient_path}}"
+ obs error:
+ covariance model: diagonal
+
+ # Observation Bias Correction (VarBC)
+ # -----------------------------------
+
+ # Observation Filters (QC)
+ # ------------------------
+ obs filters:
+ - filter: PreQC
+ maxvalue: 1
+ - filter: Domain Check
+ where:
+ - variable:
+ name: latitude@MetaData
+ minvalue: -60
+ maxvalue: 60
+ - filter: Bounds Check
+ filter variables:
+ - name: aerosolOpticalDepth
+ channels: 4
+ minvalue: 0
+ maxvalue: 4.9
+ action:
+ name: reject
+ - filter: Background Check
+ channels: 4
+ threshold: 3.0
+ action:
+ name: inflate error
+ inflation factor: 3.0
diff --git a/parm/jcb-gdas/observations/aero/retrieval_aod_viirs_npp.yaml.j2 b/parm/jcb-gdas/observations/aero/retrieval_aod_viirs_npp.yaml.j2
new file mode 100644
index 000000000..119aaf18d
--- /dev/null
+++ b/parm/jcb-gdas/observations/aero/retrieval_aod_viirs_npp.yaml.j2
@@ -0,0 +1,64 @@
+-
+
+ # Observation Space (I/O)
+ # -----------------------
+ obs space:
+ name: {{observation_from_jcb}}
+ obsdatain:
+ engine:
+ type: H5File
+ obsfile: "{{aero_obsdatain_path}}/{{aero_obsdatain_prefix}}{{observation_from_jcb}}{{aero_obsdatain_suffix}}"
+ obsdataout:
+ engine:
+ type: H5File
+ obsfile: "{{aero_obsdataout_path}}/{{aero_obsdataout_prefix}}{{observation_from_jcb}}{{aero_obsdataout_suffix}}"
+ missing file action: warn
+ io pool:
+ max pool size: 2
+ simulated variables: [aerosolOpticalDepth]
+ channels: 4
+
+ # Observation Operator
+ # --------------------
+ get values:
+ interpolation method: barycentric
+ time interpolation: linear
+ obs operator:
+ name: AodCRTM
+ Absorbers: [H2O,O3]
+ obs options:
+ Sensor_ID: &{{observation_from_jcb}}_sensor_id v.viirs-m_npp
+ EndianType: little_endian
+ AerosolOption: aerosols_gocart_default
+ CoefficientPath: "{{crtm_coefficient_path}}"
+ obs error:
+ covariance model: diagonal
+
+ # Observation Bias Correction (VarBC)
+ # -----------------------------------
+
+ # Observation Filters (QC)
+ # ------------------------
+ obs filters:
+ - filter: PreQC
+ maxvalue: 1
+ - filter: Domain Check
+ where:
+ - variable:
+ name: latitude@MetaData
+ minvalue: -60
+ maxvalue: 60
+ - filter: Bounds Check
+ filter variables:
+ - name: aerosolOpticalDepth
+ channels: 4
+ minvalue: 0
+ maxvalue: 4.9
+ action:
+ name: reject
+ - filter: Background Check
+ channels: 4
+ threshold: 3.0
+ action:
+ name: inflate error
+ inflation factor: 3.0
diff --git a/parm/jcb-gdas/observations/atmosphere-lgetkf/aircraft.yaml.j2 b/parm/jcb-gdas/observations/atmosphere-lgetkf/aircraft.yaml.j2
new file mode 100644
index 000000000..2690123e3
--- /dev/null
+++ b/parm/jcb-gdas/observations/atmosphere-lgetkf/aircraft.yaml.j2
@@ -0,0 +1,365 @@
+-
+
+ # Observation Space (I/O)
+ # -----------------------
+ obs space:
+ name: {{observation_from_jcb}}
+ distribution:
+ name: "{{distribution_type}}"
+ halo size: 1250e3
+ obsdatain:
+ engine:
+ type: H5File
+ obsfile: "{{atmosphere_obsdatain_path}}/{{atmosphere_obsdatain_prefix}}{{observation_from_jcb}}{{atmosphere_obsdatain_suffix}}"
+ obsgrouping:
+ group variables: ["stationIdentification"]
+ sort variable: "pressure"
+ sort order: "descending"
+ obsdataout:
+ engine:
+ type: H5File
+ obsfile: "{{atmosphere_obsdataout_path}}/{{atmosphere_obsdataout_prefix}}{{observation_from_jcb}}{{atmosphere_obsdataout_suffix}}"
+ io pool:
+ max pool size: 1
+ simulated variables: [windEastward, windNorthward, airTemperature, specificHumidity]
+ #
+
+ # Observation Operator
+ # --------------------
+ obs operator:
+ name: VertInterp
+ #
+
+ # Observation Filters (QC)
+ # ------------------------
+ obs filters:
+ # Observation Range Sanity Check
+ - filter: Bounds Check
+ filter variables:
+ - name: airTemperature
+ minvalue: 195
+ maxvalue: 327
+ action:
+ name: reject
+ #
+ - filter: Bounds Check
+ filter variables:
+ - name: specificHumidity
+ minvalue: 1.0E-7
+ maxvalue: 0.034999999
+ action:
+ name: reject
+ #
+ - filter: Bounds Check
+ filter variables:
+ - name: windEastward
+ - name: windNorthward
+ minvalue: -130
+ maxvalue: 130
+ action:
+ name: reject
+ #
+ - filter: Bounds Check
+ filter variables:
+ - name: windEastward
+ - name: windNorthward
+ test variables:
+ - name: ObsFunction/Velocity
+ maxvalue: 130.0
+ action:
+ name: reject
+ # Reject when pressure is less than 126 mb.
+ - filter: Bounds Check
+ filter variables:
+ - name: windEastward
+ - name: windNorthward
+ test variables:
+ - name: MetaData/pressure
+ minvalue: 12600
+ action:
+ name: reject
+ #
+ # Reject all obs with PreQC mark already set above 3
+ # - filter: PreQC
+ # maxvalue: 3
+ # action:
+ # name: reject
+ #
+ #--------------------------------------------------------------------------------------------------------------------
+ # Wind
+ #--------------------------------------------------------------------------------------------------------------------
+ #
+ # Begin by assigning all ObsError to a constant value. These will get overwritten (as needed) for specific types.
+ - filter: Perform Action
+ filter variables:
+ - name: windEastward
+ - name: windNorthward
+ action:
+ name: assign error
+ error parameter: 2.0 # 2.0 m/s
+ # Assign intial ObsError specific to AIREP/ACARS
+ - filter: Perform Action
+ filter variables:
+ - name: windEastward
+ - name: windNorthward
+ action:
+ name: assign error
+ error parameter: 3.6 # 3.6 m/s
+ where:
+ - variable:
+ name: ObsType/windEastward
+ is_in: 230
+ # Assign intial ObsError specific to AMDAR
+ - filter: Perform Action
+ filter variables:
+ - name: windEastward
+ - name: windNorthward
+ action:
+ name: assign error
+ error parameter: 3.0 # 3.0 m/s
+ where:
+ - variable:
+ name: ObsType/windEastward
+ is_in: 231
+ # Assign intial ObsError specific to MDCRS
+ - filter: Perform Action
+ filter variables:
+ - name: windEastward
+ - name: windNorthward
+ action:
+ name: assign error
+ error parameter: 2.5 # 2.5 m/s
+ where:
+ - variable:
+ name: ObsType/windEastward
+ is_in: 233
+ #
+ - filter: Perform Action
+ filter variables:
+ - name: windEastward
+ - name: windNorthward
+ action:
+ name: assign error
+ error function:
+ name: ObsFunction/ObsErrorModelStepwiseLinear
+ options:
+ xvar:
+ name: MetaData/pressure
+ xvals: [100000, 95000, 80000, 65000, 60000, 55000, 50000, 45000, 40000,
+ 35000, 30000, 25000, 20000, 15000, 10000] #Pressure (Pa)
+ errors: [1.4, 1.5, 1.6, 1.8, 1.9, 2.0, 2.1, 2.3, 2.6, 2.8, 3.0, 3.2, 2.7,
+ 2.4, 2.1]
+ # Assign the initial ObsError, based on height/pressure for RECON aircraft
+ - filter: Perform Action
+ filter variables:
+ - name: windEastward
+ - name: windNorthward
+ action:
+ name: assign error
+ error function:
+ name: ObsFunction/ObsErrorModelStepwiseLinear
+ options:
+ xvar:
+ name: MetaData/pressure
+ xvals: [70000, 65000, 60000, 55000, 50000, 45000, 40000, 35000, 30000, 25000,
+ 20000, 15000, 10000, 7500, 5000]
+ errors: [2.4, 2.5, 2.6, 2.7, 2.8, 2.95, 3.1, 3.25, 3.4, 3.175, 2.95, 2.725,
+ 2.5, 2.6, 2.7]
+ where:
+ - variable:
+ name: ObsType/windEastward
+ is_in: 232
+ # Reject when difference of wind direction is more than 50 degrees.
+ - filter: Bounds Check
+ filter variables:
+ - name: windEastward
+ - name: windNorthward
+ test variables:
+ - name: ObsFunction/WindDirAngleDiff
+ options:
+ minimum_uv: 3.5
+ maxvalue: 50.0
+ action:
+ name: reject
+ defer to post: true
+ # When multiple obs exist within a single vertical model level, inflate ObsError
+ # - filter: Perform Action
+ # filter variables:
+ # - name: windEastward
+ # action:
+ # name: inflate error
+ # inflation variable:
+ # name: ObsFunction/ObsErrorFactorConventional
+ # options:
+ # test QCflag: PreQC
+ # inflate variables: [windEastward]
+ # defer to post: true
+ #
+ # - filter: Perform Action
+ # filter variables:
+ # - name: windNorthward
+ # action:
+ # name: inflate error
+ # inflation variable:
+ # name: ObsFunction/ObsErrorFactorConventional
+ # options:
+ # test QCflag: PreQC
+ # inflate variables: [windNorthward]
+ # defer to post: true
+ #
+ # Gross error check with (O - B) / ObsError greater than threshold.
+ - filter: Background Check
+ filter variables:
+ - name: windEastward
+ - name: windNorthward
+ threshold: 6.0
+ absolute threshold: 19.0
+ action:
+ name: reject
+ #
+ #--------------------------------------------------------------------------------------------------------------------
+ # Temperature
+ #--------------------------------------------------------------------------------------------------------------------
+ #
+ # Begin by assigning all ObsError to a constant value. These will get overwritten for specific types.
+ - filter: Perform Action
+ filter variables:
+ - name: airTemperature
+ action:
+ name: assign error
+ error parameter: 2.0 # 2.0 K
+ # Assign the initial observation error, based on pressure (for AIREP/ACARS; itype=130)
+ - filter: Perform Action
+ filter variables:
+ - name: airTemperature
+ action:
+ name: assign error
+ error function:
+ name: ObsFunction/ObsErrorModelStepwiseLinear
+ options:
+ xvar:
+ name: MetaData/pressure
+ xvals: [100000, 95000, 90000, 85000, 80000]
+ errors: [2.5, 2.3, 2.1, 1.9, 1.7]
+ where:
+ - variable:
+ name: ObsType/airTemperature
+ is_in: 130
+ # Assign the initial observation error, based on pressure (for AMDAR and MDCRS; itype=131,133)
+ - filter: Perform Action
+ filter variables:
+ - name: airTemperature
+ action:
+ name: assign error
+ error function:
+ name: ObsFunction/ObsErrorModelStepwiseLinear
+ options:
+ xvar:
+ name: MetaData/pressure
+ xvals: [100000, 95000, 90000, 85000, 80000]
+ errors: [1.4706, 1.3529, 1.2353, 1.1176, 1.0]
+ where:
+ - variable:
+ name: ObsType/airTemperature
+ is_in: 131,133
+ # Assign the initial observation error, based on pressure (for RECON aircraft; itype=132)
+ - filter: Perform Action
+ filter variables:
+ - name: airTemperature
+ action:
+ name: assign error
+ error function:
+ name: ObsFunction/ObsErrorModelStepwiseLinear
+ options:
+ xvar:
+ name: MetaData/pressure
+ xvals: [100000, 95000, 90000, 85000, 35000, 30000, 25000, 20000, 15000,
+ 10000, 7500, 5000, 4000, 3200, 2000, 1000]
+ errors: [1.2, 1.1, 0.9, 0.8, 0.8, 0.9, 1.2, 1.2, 1.0, 0.8, 0.8, 0.9, 0.95,
+ 1.0, 1.25, 1.5]
+ where:
+ - variable:
+ name: ObsType/airTemperature
+ is_in: 132
+ # When multiple obs exist within a single vertical model level, inflate ObsError
+ # - filter: Perform Action
+ # filter variables:
+ # - name: airTemperature
+ # action:
+ # name: inflate error
+ # inflation variable:
+ # name: ObsFunction/ObsErrorFactorConventional
+ # options:
+ # test QCflag: PreQC
+ # inflate variables: [airTemperature]
+ # defer to post: true
+ # Gross error check with (O - B) / ObsError greater than threshold.
+ - filter: Background Check
+ filter variables:
+ - name: airTemperature
+ threshold: 7.0
+ absolute threshold: 8.0
+ action:
+ name: reject
+ #
+ #--------------------------------------------------------------------------------------------------------------------
+ # Moisture
+ #--------------------------------------------------------------------------------------------------------------------
+ #
+ # Assign the initial observation error, based on height/pressure ONLY MDCRS
+ - filter: Perform Action
+ filter variables:
+ - name: specificHumidity
+ action:
+ name: assign error
+ error function:
+ name: ObsFunction/ObsErrorModelStepwiseLinear
+ options:
+ xvar:
+ name: MetaData/pressure
+ xvals: [110000, 105000, 100000, 95000, 90000, 85000, 80000, 75000, 70000,
+ 65000, 60000, 55000, 50000, 45000, 40000, 35000, 30000, 25000, 20000,
+ 15000, 10000, 7500, 5000, 4000, 3000]
+ errors: [.19455, .19062, .18488, .17877, .17342, .16976, .16777, .16696,
+ .16605, .16522, .16637, .17086, .17791, .18492, .18996, .19294, .19447,
+ .19597, .19748, .19866, .19941, .19979, .19994, .19999, .2]
+ scale_factor_var: ObsValue/specificHumidity
+ where:
+ - variable:
+ name: ObsType/specificHumidity
+ is_in: 133
+ # When multiple obs exist within a single vertical model level, inflate ObsError
+ # - filter: Perform Action
+ # filter variables:
+ # - name: specificHumidity
+ # action:
+ # name: inflate error
+ # inflation variable:
+ # name: ObsFunction/ObsErrorFactorConventional
+ # options:
+ # test QCflag: PreQC
+ # inflate variables: [specificHumidity]
+ # defer to post: true
+ # Gross error check with (O - B) / ObsError greater than threshold.
+ - filter: Background Check
+ filter variables:
+ - name: specificHumidity
+ threshold: 8.0
+ action:
+ name: reject
+
+ # Observation Localizations (LocalEnsembleDA)
+ # -------------------------------------------
+ obs localizations:
+ - localization method: Horizontal Gaspari-Cohn
+ lengthscale: 1250e3
+ max nobs: 10000
+
+ # GeoVaLs for Driving Observation Operators (testing mode)
+ # --------------------------------------------------------
+ geovals:
+ filename: "{{atmosphere_obsdatain_path}}/{{atmosphere_obsdatain_prefix}}{{observation_from_jcb}}_geoval{{atmosphere_obsdatain_suffix}}"
+
+ # Passed benchmark for UFO testing
+ # --------------------------------
+ passedBenchmark: 0
diff --git a/parm/jcb-gdas/observations/atmosphere-lgetkf/conventional_ps.yaml.j2 b/parm/jcb-gdas/observations/atmosphere-lgetkf/conventional_ps.yaml.j2
new file mode 100644
index 000000000..a9be15805
--- /dev/null
+++ b/parm/jcb-gdas/observations/atmosphere-lgetkf/conventional_ps.yaml.j2
@@ -0,0 +1,373 @@
+-
+
+ # Observation Space (I/O)
+ # -----------------------
+ obs space:
+ name: {{observation_from_jcb}}
+ distribution:
+ name: "{{distribution_type}}"
+ halo size: 1250e3
+ obsdatain:
+ engine:
+ type: H5File
+ obsfile: "{{atmosphere_obsdatain_path}}/{{atmosphere_obsdatain_prefix}}{{observation_from_jcb}}{{atmosphere_obsdatain_suffix}}"
+ obsdataout:
+ engine:
+ type: H5File
+ obsfile: "{{atmosphere_obsdataout_path}}/{{atmosphere_obsdataout_prefix}}{{observation_from_jcb}}{{atmosphere_obsdataout_suffix}}"
+ io pool:
+ max pool size: 1
+ simulated variables: [stationPressure]
+
+ # Observation Operator
+ # --------------------
+ obs operator:
+ name: SfcCorrected
+ variables:
+ - name: stationPressure
+ correction scheme to use: GSL
+ station_altitude: height
+ geovar_sfc_geomz: height_above_mean_sea_level_at_surface
+ geovar_geomz: geopotential_height
+
+ # Linear Observation Operator
+ # ---------------------------
+ linear obs operator:
+ name: Identity
+ variables:
+ - name: stationPressure
+
+ # Observation Prior Filters (QC)
+ # ------------------------------
+ obs prior filters:
+ # Initial Error Assignments for SFC Observations
+ - filter: Perform Action
+ filter variables:
+ - name: stationPressure
+ where:
+ - variable: ObsType/stationPressure
+ is_in: [181]
+ action:
+ name: assign error
+ error function:
+ name: ObsFunction/ObsErrorModelStepwiseLinear
+ options:
+ round_to_the_nearest_integer: true
+ xvar:
+ name: ObsValue/stationPressure
+ xvals: [80000, 75000, 70000, 65000, 60000, 55000]
+ errors: [110, 120, 120, 120, 120, 1.0e+11]
+ - filter: Perform Action
+ filter variables:
+ - name: stationPressure
+ where:
+ - variable: ObsType/stationPressure
+ is_in: [187]
+ action:
+ name: assign error
+ error function:
+ name: ObsFunction/ObsErrorModelStepwiseLinear
+ options:
+ round_to_the_nearest_integer: true
+ xvar:
+ name: ObsValue/stationPressure
+ xvals: [85000, 80000, 75000, 70000, 65000, 60000, 55000]
+ errors: [120, 140, 140, 140, 140, 140, 1.0e+11]
+ # Initial Error Assignments for SFCSHIP Observations
+ - filter: Perform Action
+ filter variables:
+ - name: stationPressure
+ where:
+ - variable: ObsType/stationPressure
+ is_in: [180]
+ action:
+ name: assign error
+ error function:
+ name: ObsFunction/ObsErrorModelStepwiseLinear
+ options:
+ round_to_the_nearest_integer: true
+ xvar:
+ name: ObsValue/stationPressure
+ xvals: [60000, 55000]
+ errors: [130, 1.0e+11]
+ - filter: Perform Action
+ filter variables:
+ - name: stationPressure
+ where:
+ - variable: ObsType/stationPressure
+ is_in: [183]
+ action:
+ name: assign error
+ error parameter: 1.0e+11
+
+ # Initial Error Assignments for Radiosonde
+ - filter: Perform Action
+ filter variables:
+ - name: stationPressure
+ where:
+ - variable: ObsType/stationPressure
+ is_in: [120]
+ action:
+ name: assign error
+ error function:
+ name: ObsFunction/ObsErrorModelStepwiseLinear
+ options:
+ round_to_the_nearest_integer: true
+ xvar:
+ name: ObsValue/stationPressure
+ xvals: [80000, 75000, 70000, 65000, 60000, 55000]
+ errors: [110, 120, 120, 120, 120, 1.0e+11]
+ # Create PreQC group variable (pqm in GSI read_prepbufr)
+ - filter: Variable Assignment
+ assignments:
+ - name: InputObsError/stationPressure
+ type: float
+ source variable: ObsErrorData/stationPressure
+
+ # Set observation quality-realted variables
+ # Create PreQC group variable (pqm in GSI read_prepbufr)
+ - filter: Variable Assignment
+ assignments:
+ - name: PreQC/stationPressure
+ type: int
+ source variable: QualityMarker/stationPressure
+
+ # Create PreUseFlag group variable (usage in GSI read_prepbufr)
+ # Initialize
+ - filter: Variable Assignment
+ assignments:
+ - name: PreUseFlag/stationPressure
+ type: int
+ source variable: PreQC/stationPressure
+
+ - filter: Variable Assignment
+ where:
+ - variable:
+ name: PreUseFlag/stationPressure
+ is_in: 1-15
+ assignments:
+ - name: PreUseFlag/stationPressure
+ value: 0
+ # Re-assignment
+ - filter: Variable Assignment
+ where:
+ - variable:
+ name: ObsType/stationPressure
+ is_in: 183
+ assignments:
+ - name: PreUseFlag/stationPressure
+ value: 100
+
+ - filter: Variable Assignment
+ where:
+ - variable:
+ name: ObsValue/stationPressure
+ is_defined:
+ - variable:
+ name: ObsValue/stationPressure
+ maxvalue: 50000.00
+ where operator: and
+ assignments:
+ - name: PreUseFlag/stationPressure
+ value: 100
+
+ - filter: Variable Assignment
+ where:
+ - variable:
+ name: PreQC/stationPressure
+ is_in: 9, 12, 15
+ assignments:
+ - name: PreUseFlag/stationPressure
+ value: 100
+
+ - filter: Variable Assignment
+ where:
+ - variable:
+ name: PreQC/stationPressure
+ is_in: 4-15
+ assignments:
+ - name: PreUseFlag/stationPressure
+ value: 101
+
+ ## Observation range sanity check
+ #- filter: Bounds Check
+ # filter variables:
+ # - name: stationPressure
+ # minvalue: 37499.0
+ # maxvalue: 106999.0
+ # action:
+ # name: reject
+ ## Reject all ObsType 183
+ #- filter: RejectList
+ # where:
+ # - variable:
+ # name: ObsType/stationPressure
+ # is_in: 183
+ ## Reject surface pressure below 500 hPa
+ #- filter: Bounds Check
+ # filter variables:
+ # - name: stationPressure
+ # minvalue: 50000.00
+ # action:
+ # name: reject
+ #- filter: RejectList
+ # where:
+ # - variable:
+ # name: PreQC/stationPressure
+ # is_in: 4-15
+ # Inflate obs error based on obs type
+ - filter: Perform Action
+ filter variables:
+ - name: stationPressure
+ where:
+ - variable: PreQC/stationPressure
+ is_in: 3, 7
+ action:
+ name: inflate error
+ inflation factor: 1.2
+
+ # Observation Post Filters (QC)
+ # -----------------------------
+ obs post filters:
+ # Calculate obs error inflation factors for duplicated observations at the same location
+ - filter: Variable Assignment
+ assignments:
+ - name: ObsErrorFactorDuplicateCheck/stationPressure
+ type: float
+ function:
+ name: ObsFunction/ObsErrorFactorDuplicateCheck
+ options:
+ use_air_pressure: false
+ variable: stationPressure
+
+ # Reduce effective observation error based on obs type and subtype
+ # In this case: reduce effective obs error for buoy
+ - filter: Perform Action
+ filter variables:
+ - name: stationPressure
+ where:
+ - variable:
+ name: ObsType/stationPressure
+ is_in: 180
+ - variable:
+ name: ObsSubType/stationPressure
+ is_in: 0
+ action:
+ name: inflate error
+ inflation factor: 0.7
+
+ # Calculate obs error inflation factors for large discrepancies between model and observations
+ - filter: Variable Assignment
+ assignments:
+ - name: ObsErrorFactorSfcPressure/stationPressure
+ type: float
+ function:
+ name: ObsFunction/ObsErrorFactorSfcPressure
+ options:
+ geovar_sfc_geomz: height_above_mean_sea_level_at_surface
+ geovar_geomz: geopotential_height
+ station_altitude: height
+
+ # Inflate surface pressure observation based on discrepancies between
+ # model and observations due to terrian
+ - filter: Perform Action
+ filter variables:
+ - name: stationPressure
+ action:
+ name: inflate error
+ inflation variable:
+ name: ObsErrorFactorSfcPressure/stationPressure
+
+ - filter: Variable Assignment
+ assignments:
+ - name: DerivedMetaData/Innovation
+ type: float
+ function:
+ name: ObsFunction/Arithmetic
+ options:
+ variables:
+ - name: ObsValue/stationPressure
+ - name: HofX/stationPressure
+ coefs: [1, -1]
+ - filter: Variable Assignment
+ assignments:
+ - name: DerivedMetaData/ObsErrorBoundSfcPressure1
+ type: float
+ function:
+ name: ObsFunction/ObsErrorBoundConventional
+ options:
+ obsvar: stationPressure
+ obserr_bound_min: 100
+ obserr_bound_max: 300
+ obserr_bound_factor: 5.0
+
+ - filter: Background Check
+ filter variables:
+ - name: stationPressure
+ where:
+ - variable: PreQC/stationPressure
+ is_not_in: 3
+ function absolute threshold:
+ - name: DerivedMetaData/ObsErrorBoundSfcPressure1
+ action:
+ name: reject
+
+ - filter: Variable Assignment
+ assignments:
+ - name: DerivedMetaData/ObsErrorBoundSfcPressure2
+ type: float
+ function:
+ name: ObsFunction/ObsErrorBoundConventional
+ options:
+ obsvar: stationPressure
+ obserr_bound_min: 100
+ obserr_bound_max: 300
+ obserr_bound_factor: 3.5
+
+ - filter: Background Check
+ filter variables:
+ - name: stationPressure
+ where:
+ - variable: PreQC/stationPressure
+ is_in: 3
+ function absolute threshold:
+ - name: DerivedMetaData/ObsErrorBoundSfcPressure2
+ action:
+ name: reject
+
+ # Inflate obs error based on duplicate check
+ - filter: Perform Action
+ filter variables:
+ - name: stationPressure
+ action:
+ name: inflate error
+ inflation variable:
+ name: ObsErrorFactorDuplicateCheck/stationPressure
+
+ # Reject data based on PreUseFlag (usage in GSI)
+ - filter: Perform Action
+ filter variables:
+ - name: stationPressure
+ where:
+ - variable: PreUseFlag/stationPressure
+ is_not_in: 0, 1
+ action:
+ name: reject
+ # End of Filters
+
+ # Observation Localizations (LocalEnsembleDA)
+ # -------------------------------------------
+ obs localizations:
+ - localization method: Horizontal Gaspari-Cohn
+ lengthscale: 1250e3
+ max nobs: 10000
+
+
+ # GeoVaLs for Driving Observation Operators (testing mode)
+ # --------------------------------------------------------
+ geovals:
+ filename: "{{atmosphere_obsdatain_path}}/{{atmosphere_obsdatain_prefix}}{{observation_from_jcb}}_geoval{{atmosphere_obsdatain_suffix}}"
+
+ # Passed benchmark for UFO testing
+ # --------------------------------
+ passedBenchmark: 0
diff --git a/parm/jcb-gdas/observations/atmosphere-lgetkf/gnssro.yaml.j2 b/parm/jcb-gdas/observations/atmosphere-lgetkf/gnssro.yaml.j2
new file mode 100644
index 000000000..df980564e
--- /dev/null
+++ b/parm/jcb-gdas/observations/atmosphere-lgetkf/gnssro.yaml.j2
@@ -0,0 +1,167 @@
+-
+
+ # Observation Space (I/O)
+ # -----------------------
+ obs space:
+ name: {{observation_from_jcb}}
+ distribution:
+ name: "{{distribution_type}}"
+ halo size: 1250e3
+ obsdatain:
+ engine:
+ type: H5File
+ obsfile: "{{atmosphere_obsdatain_path}}/{{atmosphere_obsdatain_prefix}}{{observation_from_jcb}}{{atmosphere_obsdatain_suffix}}"
+ # obsgrouping:
+ # group variables: [ "sequenceNumber" ]
+ # sort variable: "impactHeightRO"
+ # sort order: "ascending"
+ obsdataout:
+ engine:
+ type: H5File
+ obsfile: "{{atmosphere_obsdataout_path}}/{{atmosphere_obsdataout_prefix}}{{observation_from_jcb}}{{atmosphere_obsdataout_suffix}}"
+ simulated variables: [bendingAngle]
+
+ # Observation Operator
+ # --------------------
+ obs operator:
+ name: GnssroBndNBAM
+ obs options:
+ use_compress: 1
+ sr_steps: 2
+ vertlayer: full
+ super_ref_qc: NBAM
+
+ # Observation Filters (QC)
+ # ------------------------
+ obs filters:
+ # Apply gross check using pccf
+ # Step 0-A: Create Diagnostic Flags
+ # Diagnostic flag for pccf
+ - filter: Create Diagnostic Flags
+ filter variables:
+ - name: bendingAngle
+ flags:
+ - name: pccfCheckReject
+ initial value: false
+ force reinitialization: true
+
+ # Diagnostic flag for qfro
+ - filter: Create Diagnostic Flags
+ filter variables:
+ - name: bendingAngle
+ flags:
+ - name: qfroCheckReject
+ initial value: false
+ force reinitialization: true
+
+ # Step 0-B: pccf Check - good: 0.1-100, reject: 0
+ - filter: Bounds Check
+ filter variables:
+ - name: bendingAngle
+ where:
+ - variable:
+ name: MetaData/satelliteIdentifier
+ is_in: 265-269,750-755,44,786,820,825
+ test variables:
+ - name: MetaData/pccf
+ minvalue: 0.1
+ maxvalue: 100.1
+ actions:
+ - name: set
+ flag: pccfCheckReject
+ - name: reject
+
+ # Step 0-B: qfro Check - good: 0, reject: 1
+ - filter: Bounds Check
+ - filter: RejectList
+ filter variables:
+ - name: bendingAngle
+ where:
+ - variable:
+ name: MetaData/satelliteIdentifier
+ is_in: 3-5,421,440,821
+ test variables:
+ - name: MetaData/qualityFlags
+ minvalue: -0.1
+ maxvalue: 0.1
+ actions:
+ - name: set
+ flag: qfroCheckReject
+ - name: reject
+
+ #1. gpstop
+ - filter: Domain Check
+ filter variables:
+ - name: bendingAngle
+ where:
+ - variable:
+ name: MetaData/impactHeightRO
+ minvalue: 0
+ maxvalue: 55000.1
+ action:
+ name: reject
+ #2. commgpstop
+ - filter: Bounds Check
+ filter variables:
+ - name: bendingAngle
+ where:
+ - variable:
+ name: MetaData/satelliteIdentifier
+ is_in: 265,266,267,268,269
+ test variables:
+ - name: MetaData/impactHeightRO
+ maxvalue: 45000.1
+ action:
+ name: reject
+ #3. metop below 8 km
+ - filter: Bounds Check
+ filter variables:
+ - name: bendingAngle
+ where:
+ - variable:
+ name: MetaData/satelliteIdentifier
+ is_in: 3-5
+ test variables:
+ - name: MetaData/impactHeightRO
+ minvalue: 8000.1
+ action:
+ name: reject
+ #4. assign obs error
+ - filter: ROobserror
+ filter variables:
+ - name: bendingAngle
+ errmodel: NBAM
+ #5. RONBAM cut off check
+ - filter: Background Check RONBAM
+ filter variables:
+ - name: bendingAngle
+ #6. Obs error inflate
+ - filter: Background Check RONBAM
+ filter variables:
+ - name: bendingAngle
+ action:
+ name: RONBAMErrInflate
+ #7. Background check
+ #- filter: Background Check
+ # filter variables:
+ # - name: bendingAngle
+ # threshold: 10
+ # action:
+ # name: reject
+
+ # Observation Localizations (LocalEnsembleDA)
+ # -------------------------------------------
+ obs localizations:
+ - localization method: Horizontal Gaspari-Cohn
+ lengthscale: 1250e3
+ max nobs: 10000
+
+
+ # GeoVaLs for Driving Observation Operators (testing mode)
+ # --------------------------------------------------------
+ geovals:
+ filename: "{{atmosphere_obsdatain_path}}/{{atmosphere_obsdatain_prefix}}{{observation_from_jcb}}_geoval{{atmosphere_obsdatain_suffix}}"
+
+ # Passed benchmark for UFO testing
+ # --------------------------------
+ passedBenchmark: 0
diff --git a/parm/jcb-gdas/observations/atmosphere-lgetkf/gnssro_cosmic2.yaml.j2 b/parm/jcb-gdas/observations/atmosphere-lgetkf/gnssro_cosmic2.yaml.j2
new file mode 100644
index 000000000..8651b324e
--- /dev/null
+++ b/parm/jcb-gdas/observations/atmosphere-lgetkf/gnssro_cosmic2.yaml.j2
@@ -0,0 +1,104 @@
+-
+
+ # Observation Space (I/O)
+ # -----------------------
+ obs space:
+ name: {{observation_from_jcb}}
+ distribution:
+ name: "{{distribution_type}}"
+ halo size: 1250e3
+ obsdatain:
+ engine:
+ type: H5File
+ obsfile: "{{atmosphere_obsdatain_path}}/{{atmosphere_obsdatain_prefix}}{{observation_from_jcb}}{{atmosphere_obsdatain_suffix}}"
+ obsgrouping:
+ group variables: [ 'sequenceNumber' ]
+ sort variable: 'impactHeightRO'
+ sort order: 'ascending'
+ obsdataout:
+ engine:
+ type: H5File
+ obsfile: "{{atmosphere_obsdataout_path}}/{{atmosphere_obsdataout_prefix}}{{observation_from_jcb}}{{atmosphere_obsdataout_suffix}}"
+ simulated variables: [bendingAngle]
+
+ # Observation Operator
+ # --------------------
+ obs operator:
+ name: GnssroBndNBAM
+ obs options:
+ use_compress: 1
+ sr_steps: 2
+ vertlayer: full
+ super_ref_qc: NBAM
+ output_diags: true
+
+ # Observation Filters (QC)
+ # ------------------------
+ obs filters:
+ # Apply gross check using pccf
+ # Step 0-A: Create Diagnostic Flags
+ # Diagnostic flag for pccf
+ - filter: Create Diagnostic Flags
+ filter variables:
+ - name: bendingAngle
+ flags:
+ - name: pccfCheckReject
+ initial value: false
+ force reinitialization: true
+
+ # Step 0-B: pccf Check for CDACC data - good: 0.1-100, reject: 0
+ - filter: Bounds Check
+ filter variables:
+ - name: bendingAngle
+ where:
+ - variable:
+ name: MetaData/satelliteIdentifier
+ is_in: 265-269,750-755,44,786,820,825
+ test variables:
+ - name: MetaData/pccf
+ minvalue: 0.1
+ maxvalue: 100.1
+ actions:
+ - name: set
+ flag: pccfCheckReject
+ - name: reject
+
+ #1. gpstop
+ - filter: Domain Check
+ filter variables:
+ - name: bendingAngle
+ where:
+ - variable:
+ name: MetaData/impactHeightRO
+ minvalue: 0
+ maxvalue: 55000.1
+ action:
+ name: reject
+ #3. RONBAM cut off check
+ - filter: Background Check RONBAM
+ filter variables:
+ - name: bendingAngle
+ action:
+ name: reject
+ defer to post: true
+ #4. assign obs error
+ - filter: ROobserror
+ filter variables:
+ - name: bendingAngle
+ errmodel: NBAM
+ defer to post: true
+ #5. Obs error inflate
+ - filter: Perform Action
+ filter variables:
+ - name: bendingAngle
+ action:
+ name: RONBAMErrInflate
+ defer to post: true
+ # --------------------------------
+
+ # Observation Localizations (LocalEnsembleDA)
+ # -------------------------------------------
+ obs localizations:
+ - localization method: Horizontal Gaspari-Cohn
+ lengthscale: 1250e3
+ max obs: 10000
diff --git a/parm/jcb-gdas/observations/atmosphere-lgetkf/sondes.yaml.j2 b/parm/jcb-gdas/observations/atmosphere-lgetkf/sondes.yaml.j2
new file mode 100644
index 000000000..3064438f6
--- /dev/null
+++ b/parm/jcb-gdas/observations/atmosphere-lgetkf/sondes.yaml.j2
@@ -0,0 +1,59 @@
+-
+
+ # Observation Space (I/O)
+ # -----------------------
+ obs space:
+ name: {{observation_from_jcb}}
+ distribution:
+ name: "{{distribution_type}}"
+ halo size: 1250e3
+ obsdatain:
+ engine:
+ type: H5File
+ obsfile: "{{atmosphere_obsdatain_path}}/{{atmosphere_obsdatain_prefix}}{{observation_from_jcb}}{{atmosphere_obsdatain_suffix}}"
+ obsdataout:
+ engine:
+ type: H5File
+ obsfile: "{{atmosphere_obsdataout_path}}/{{atmosphere_obsdataout_prefix}}{{observation_from_jcb}}{{atmosphere_obsdataout_suffix}}"
+ io pool:
+ max pool size: 1
+ simulated variables: [windEastward, windNorthward, airTemperature]
+
+ # Observation Operator
+ # --------------------
+ obs operator:
+ name: VertInterp
+
+ # Observation Error
+ # -----------------
+ obs error:
+ covariance model: diagonal
+
+ # Observation Filters (QC)
+ # ------------------------
+ obs filters:
+ - filter: PreQC
+ maxvalue: 3
+ - filter: Background Check
+ filter variables:
+ - name: windEastward
+ - name: windNorthward
+ - name: airTemperature
+ threshold: 2.0
+
+ # Observation Localizations (LocalEnsembleDA)
+ # -------------------------------------------
+ obs localizations:
+ - localization method: Horizontal Gaspari-Cohn
+ lengthscale: 1250e3
+ max nobs: 10000
+
+
+ # GeoVaLs for Driving Observation Operators (testing mode)
+ # --------------------------------------------------------
+ geovals:
+ filename: "{{atmosphere_obsdatain_path}}/{{atmosphere_obsdatain_prefix}}{{observation_from_jcb}}_geoval{{atmosphere_obsdatain_suffix}}"
+
+ # Passed benchmark for UFO testing
+ # --------------------------------
+ passedBenchmark: 0
diff --git a/parm/jcb-gdas/observations/atmosphere/conventional_ps.yaml.j2 b/parm/jcb-gdas/observations/atmosphere/conventional_ps.yaml.j2
new file mode 100644
index 000000000..f870262ad
--- /dev/null
+++ b/parm/jcb-gdas/observations/atmosphere/conventional_ps.yaml.j2
@@ -0,0 +1,369 @@
+-
+
+ # Observation Space (I/O)
+ # -----------------------
+ obs space:
+ name: {{observation_from_jcb}}
+ obsdatain:
+ engine:
+ type: H5File
+ obsfile: "{{atmosphere_obsdatain_path}}/{{atmosphere_obsdatain_prefix}}{{observation_from_jcb}}{{atmosphere_obsdatain_suffix}}"
+ missing file action: warn
+ obsdataout:
+ engine:
+ type: H5File
+ obsfile: "{{atmosphere_obsdataout_path}}/{{atmosphere_obsdataout_prefix}}{{observation_from_jcb}}{{atmosphere_obsdataout_suffix}}"
+ io pool:
+ max pool size: 1
+ simulated variables: [stationPressure]
+
+ # Observation Operator
+ # --------------------
+ obs operator:
+ name: SfcCorrected
+ variables:
+ - name: stationPressure
+ correction scheme to use: GSL
+ station_altitude: height
+ geovar_sfc_geomz: height_above_mean_sea_level_at_surface
+ geovar_geomz: geopotential_height
+
+ # Linear Observation Operator
+ # ---------------------------
+ linear obs operator:
+ name: Identity
+ variables:
+ - name: stationPressure
+
+ # Observation Prior Filters (QC)
+ # ------------------------------
+ obs prior filters:
+ # Initial Error Assignments for SFC Observations
+ - filter: Perform Action
+ filter variables:
+ - name: stationPressure
+ where:
+ - variable: ObsType/stationPressure
+ is_in: [181]
+ action:
+ name: assign error
+ error function:
+ name: ObsFunction/ObsErrorModelStepwiseLinear
+ options:
+ round_to_the_nearest_integer: true
+ xvar:
+ name: ObsValue/stationPressure
+ xvals: [80000, 75000, 70000, 65000, 60000, 55000]
+ errors: [110, 120, 120, 120, 120, 1.0e+11]
+
+ - filter: Perform Action
+ filter variables:
+ - name: stationPressure
+ where:
+ - variable: ObsType/stationPressure
+ is_in: [187]
+ action:
+ name: assign error
+ error function:
+ name: ObsFunction/ObsErrorModelStepwiseLinear
+ options:
+ round_to_the_nearest_integer: true
+ xvar:
+ name: ObsValue/stationPressure
+ xvals: [85000, 80000, 75000, 70000, 65000, 60000, 55000]
+ errors: [120, 140, 140, 140, 140, 140, 1.0e+11]
+
+ # Initial Error Assignments for SFCSHIP Observations
+ - filter: Perform Action
+ filter variables:
+ - name: stationPressure
+ where:
+ - variable: ObsType/stationPressure
+ is_in: [180]
+ action:
+ name: assign error
+ error function:
+ name: ObsFunction/ObsErrorModelStepwiseLinear
+ options:
+ round_to_the_nearest_integer: true
+ xvar:
+ name: ObsValue/stationPressure
+ xvals: [60000, 55000]
+ errors: [130, 1.0e+11]
+
+ - filter: Perform Action
+ filter variables:
+ - name: stationPressure
+ where:
+ - variable: ObsType/stationPressure
+ is_in: [183]
+ action:
+ name: assign error
+ error parameter: 1.0e+11
+
+ # Initial Error Assignments for Radiosonde
+ - filter: Perform Action
+ filter variables:
+ - name: stationPressure
+ where:
+ - variable: ObsType/stationPressure
+ is_in: [120]
+ action:
+ name: assign error
+ error function:
+ name: ObsFunction/ObsErrorModelStepwiseLinear
+ options:
+ round_to_the_nearest_integer: true
+ xvar:
+ name: ObsValue/stationPressure
+ xvals: [80000, 75000, 70000, 65000, 60000, 55000]
+ errors: [110, 120, 120, 120, 120, 1.0e+11]
+
+ # Create PreQC group variable (pqm in GSI read_prepbufr)
+ - filter: Variable Assignment
+ assignments:
+ - name: InputObsError/stationPressure
+ type: float
+ source variable: ObsErrorData/stationPressure
+
+ # Set observation quality-realted variables
+ # Create PreQC group variable (pqm in GSI read_prepbufr)
+ - filter: Variable Assignment
+ assignments:
+ - name: PreQC/stationPressure
+ type: int
+ source variable: QualityMarker/stationPressure
+
+ # Create PreUseFlag group variable (usage in GSI read_prepbufr)
+ # Initialize
+ - filter: Variable Assignment
+ assignments:
+ - name: PreUseFlag/stationPressure
+ type: int
+ source variable: PreQC/stationPressure
+
+ - filter: Variable Assignment
+ where:
+ - variable:
+ name: PreUseFlag/stationPressure
+ is_in: 1-15
+ assignments:
+ - name: PreUseFlag/stationPressure
+ value: 0
+ # Re-assignment
+ - filter: Variable Assignment
+ where:
+ - variable:
+ name: ObsType/stationPressure
+ is_in: 183
+ assignments:
+ - name: PreUseFlag/stationPressure
+ value: 100
+
+ - filter: Variable Assignment
+ where:
+ - variable:
+ name: ObsValue/stationPressure
+ is_defined:
+ - variable:
+ name: ObsValue/stationPressure
+ maxvalue: 50000.00
+ where operator: and
+ assignments:
+ - name: PreUseFlag/stationPressure
+ value: 100
+
+ - filter: Variable Assignment
+ where:
+ - variable:
+ name: PreQC/stationPressure
+ is_in: 9, 12, 15
+ assignments:
+ - name: PreUseFlag/stationPressure
+ value: 100
+
+ - filter: Variable Assignment
+ where:
+ - variable:
+ name: PreQC/stationPressure
+ is_in: 4-15
+ assignments:
+ - name: PreUseFlag/stationPressure
+ value: 101
+
+ ## Observation range sanity check
+ #- filter: Bounds Check
+ # filter variables:
+ # - name: stationPressure
+ # minvalue: 37499.0
+ # maxvalue: 106999.0
+ # action:
+ # name: reject
+ ## Reject all ObsType 183
+ #- filter: RejectList
+ # where:
+ # - variable:
+ # name: ObsType/stationPressure
+ # is_in: 183
+ ## Reject surface pressure below 500 hPa
+ #- filter: Bounds Check
+ # filter variables:
+ # - name: stationPressure
+ # minvalue: 50000.00
+ # action:
+ # name: reject
+ #- filter: RejectList
+ # where:
+ # - variable:
+ # name: PreQC/stationPressure
+ # is_in: 4-15
+ # Inflate obs error based on obs type
+ - filter: Perform Action
+ filter variables:
+ - name: stationPressure
+ where:
+ - variable: PreQC/stationPressure
+ is_in: 3, 7
+ action:
+ name: inflate error
+ inflation factor: 1.2
+
+ # Observation Post Filters (QC)
+ # -----------------------------
+ obs post filters:
+ # Calculate obs error inflation factors for duplicated observations at the same location
+ - filter: Variable Assignment
+ assignments:
+ - name: ObsErrorFactorDuplicateCheck/stationPressure
+ type: float
+ function:
+ name: ObsFunction/ObsErrorFactorDuplicateCheck
+ options:
+ use_air_pressure: false
+ variable: stationPressure
+
+ # Reduce effective observation error based on obs type and subtype
+ # In this case: reduce effective obs error for buoy
+ - filter: Perform Action
+ filter variables:
+ - name: stationPressure
+ where:
+ - variable:
+ name: ObsType/stationPressure
+ is_in: 180
+ - variable:
+ name: ObsSubType/stationPressure
+ is_in: 0
+ action:
+ name: inflate error
+ inflation factor: 0.7
+
+ # Calculate obs error inflation factors for large discrepancies between model and observations
+ - filter: Variable Assignment
+ assignments:
+ - name: ObsErrorFactorSfcPressure/stationPressure
+ type: float
+ function:
+ name: ObsFunction/ObsErrorFactorSfcPressure
+ options:
+ geovar_sfc_geomz: height_above_mean_sea_level_at_surface
+ geovar_geomz: geopotential_height
+ station_altitude: height
+
+ # Inflate surface pressure observation based on discrepancies between
+ # model and observations due to terrian
+ - filter: Perform Action
+ filter variables:
+ - name: stationPressure
+ action:
+ name: inflate error
+ inflation variable:
+ name: ObsErrorFactorSfcPressure/stationPressure
+
+ - filter: Variable Assignment
+ assignments:
+ - name: DerivedMetaData/Innovation
+ type: float
+ function:
+ name: ObsFunction/Arithmetic
+ options:
+ variables:
+ - name: ObsValue/stationPressure
+ - name: HofX/stationPressure
+ coefs: [1, -1]
+
+ - filter: Variable Assignment
+ assignments:
+ - name: DerivedMetaData/ObsErrorBoundSfcPressure1
+ type: float
+ function:
+ name: ObsFunction/ObsErrorBoundConventional
+ options:
+ obsvar: stationPressure
+ obserr_bound_min: 100
+ obserr_bound_max: 300
+ obserr_bound_factor: 5.0
+
+ - filter: Background Check
+ filter variables:
+ - name: stationPressure
+ where:
+ - variable: PreQC/stationPressure
+ is_not_in: 3
+ function absolute threshold:
+ - name: DerivedMetaData/ObsErrorBoundSfcPressure1
+ action:
+ name: reject
+
+ - filter: Variable Assignment
+ assignments:
+ - name: DerivedMetaData/ObsErrorBoundSfcPressure2
+ type: float
+ function:
+ name: ObsFunction/ObsErrorBoundConventional
+ options:
+ obsvar: stationPressure
+ obserr_bound_min: 100
+ obserr_bound_max: 300
+ obserr_bound_factor: 3.5
+
+ - filter: Background Check
+ filter variables:
+ - name: stationPressure
+ where:
+ - variable: PreQC/stationPressure
+ is_in: 3
+ function absolute threshold:
+ - name: DerivedMetaData/ObsErrorBoundSfcPressure2
+ action:
+ name: reject
+
+ # Inflate obs error based on duplicate check
+ - filter: Perform Action
+ filter variables:
+ - name: stationPressure
+ action:
+ name: inflate error
+ inflation variable:
+ name: ObsErrorFactorDuplicateCheck/stationPressure
+
+ # Reject data based on PreUseFlag (usage in GSI)
+ - filter: Perform Action
+ filter variables:
+ - name: stationPressure
+ where:
+ - variable: PreUseFlag/stationPressure
+ is_not_in: 0, 1
+ action:
+ name: reject
+ # End of Filters
+
+
+ # GeoVaLs for Driving Observation Operators (testing mode)
+ # --------------------------------------------------------
+ geovals:
+ filename: "{{atmosphere_obsdatain_path}}/{{atmosphere_obsdatain_prefix}}{{observation_from_jcb}}_geoval{{atmosphere_obsdatain_suffix}}"
+
+ # Passed benchmark for UFO testing
+ # --------------------------------
+ passedBenchmark: 0
\ No newline at end of file
diff --git a/parm/jcb-gdas/observations/atmosphere/gnssro.yaml.j2 b/parm/jcb-gdas/observations/atmosphere/gnssro.yaml.j2
new file mode 100644
index 000000000..ed5355799
--- /dev/null
+++ b/parm/jcb-gdas/observations/atmosphere/gnssro.yaml.j2
@@ -0,0 +1,158 @@
+-
+
+ # Observation Space (I/O)
+ # -----------------------
+ obs space:
+ name: {{observation_from_jcb}}
+ obsdatain:
+ engine:
+ type: H5File
+ obsfile: "{{atmosphere_obsdatain_path}}/{{atmosphere_obsdatain_prefix}}{{observation_from_jcb}}{{atmosphere_obsdatain_suffix}}"
+ missing file action: warn
+ # obsgrouping:
+ # group variables: [ "sequenceNumber" ]
+ # sort variable: "impactHeightRO"
+ # sort order: "ascending"
+ obsdataout:
+ engine:
+ type: H5File
+ obsfile: "{{atmosphere_obsdataout_path}}/{{atmosphere_obsdataout_prefix}}{{observation_from_jcb}}{{atmosphere_obsdataout_suffix}}"
+ simulated variables: [bendingAngle]
+
+ # Observation Operator
+ # --------------------
+ obs operator:
+ name: GnssroBndNBAM
+ obs options:
+ use_compress: 1
+ sr_steps: 2
+ vertlayer: full
+ super_ref_qc: NBAM
+
+ # Observation Filters (QC)
+ # ------------------------
+ obs filters:
+ # Apply gross check using pccf
+ # Step 0-A: Create Diagnostic Flags
+ # Diagnostic flag for pccf
+ - filter: Create Diagnostic Flags
+ filter variables:
+ - name: bendingAngle
+ flags:
+ - name: pccfCheckReject
+ initial value: false
+ force reinitialization: true
+
+ # Diagnostic flag for qfro
+ - filter: Create Diagnostic Flags
+ filter variables:
+ - name: bendingAngle
+ flags:
+ - name: qfroCheckReject
+ initial value: false
+ force reinitialization: true
+
+ # Step 0-B: pccf Check - good: 0.1-100, reject: 0
+ - filter: Bounds Check
+ filter variables:
+ - name: bendingAngle
+ where:
+ - variable:
+ name: MetaData/satelliteIdentifier
+ is_in: 265-269,750-755,44,786,820,825
+ test variables:
+ - name: MetaData/pccf
+ minvalue: 0.1
+ maxvalue: 100.1
+ actions:
+ - name: set
+ flag: pccfCheckReject
+ - name: reject
+
+ # Step 0-B: qfro Check - good: 0, reject: 1
+ - filter: Bounds Check
+ - filter: RejectList
+ filter variables:
+ - name: bendingAngle
+ where:
+ - variable:
+ name: MetaData/satelliteIdentifier
+ is_in: 3-5,421,440,821
+ test variables:
+ - name: MetaData/qualityFlags
+ minvalue: -0.1
+ maxvalue: 0.1
+ actions:
+ - name: set
+ flag: qfroCheckReject
+ - name: reject
+
+ #1. gpstop
+ - filter: Domain Check
+ filter variables:
+ - name: bendingAngle
+ where:
+ - variable:
+ name: MetaData/impactHeightRO
+ minvalue: 0
+ maxvalue: 55000.1
+ action:
+ name: reject
+ #2. commgpstop
+ - filter: Bounds Check
+ filter variables:
+ - name: bendingAngle
+ where:
+ - variable:
+ name: MetaData/satelliteIdentifier
+ is_in: 265,266,267,268,269
+ test variables:
+ - name: MetaData/impactHeightRO
+ maxvalue: 45000.1
+ action:
+ name: reject
+ #3. metop below 8 km
+ - filter: Bounds Check
+ filter variables:
+ - name: bendingAngle
+ where:
+ - variable:
+ name: MetaData/satelliteIdentifier
+ is_in: 3-5
+ test variables:
+ - name: MetaData/impactHeightRO
+ minvalue: 8000.1
+ action:
+ name: reject
+ #4. assign obs error
+ - filter: ROobserror
+ filter variables:
+ - name: bendingAngle
+ errmodel: NBAM
+ #5. RONBAM cut off check
+ - filter: Background Check RONBAM
+ filter variables:
+ - name: bendingAngle
+ #6. Obs error inflate
+ - filter: Background Check RONBAM
+ filter variables:
+ - name: bendingAngle
+ action:
+ name: RONBAMErrInflate
+ #7. Background check
+ #- filter: Background Check
+ # filter variables:
+ # - name: bendingAngle
+ # threshold: 10
+ # action:
+ # name: reject
+
+
+ # GeoVaLs for Driving Observation Operators (testing mode)
+ # --------------------------------------------------------
+ geovals:
+ filename: "{{atmosphere_obsdatain_path}}/{{atmosphere_obsdatain_prefix}}{{observation_from_jcb}}_geoval{{atmosphere_obsdatain_suffix}}"
+
+ # Passed benchmark for UFO testing
+ # --------------------------------
+ passedBenchmark: 0
diff --git a/parm/jcb-gdas/observations/atmosphere/gnssro_cosmic2.yaml.j2 b/parm/jcb-gdas/observations/atmosphere/gnssro_cosmic2.yaml.j2
new file mode 100644
index 000000000..f4dd7c9ad
--- /dev/null
+++ b/parm/jcb-gdas/observations/atmosphere/gnssro_cosmic2.yaml.j2
@@ -0,0 +1,95 @@
+-
+
+ # Observation Space (I/O)
+ # -----------------------
+ obs space:
+ name: {{observation_from_jcb}}
+ obsdatain:
+ engine:
+ type: H5File
+ obsfile: "{{atmosphere_obsdatain_path}}/{{atmosphere_obsdatain_prefix}}{{observation_from_jcb}}{{atmosphere_obsdatain_suffix}}"
+ missing file action: warn
+ obsgrouping:
+ group variables: [ 'sequenceNumber' ]
+ sort variable: 'impactHeightRO'
+ sort order: 'ascending'
+ obsdataout:
+ engine:
+ type: H5File
+ obsfile: "{{atmosphere_obsdataout_path}}/{{atmosphere_obsdataout_prefix}}{{observation_from_jcb}}{{atmosphere_obsdataout_suffix}}"
+ simulated variables: [bendingAngle]
+
+ # Observation Operator
+ # --------------------
+ obs operator:
+ name: GnssroBndNBAM
+ obs options:
+ use_compress: 1
+ sr_steps: 2
+ vertlayer: full
+ super_ref_qc: NBAM
+ output_diags: true
+
+ # Observation Filters (QC)
+ # ------------------------
+ obs filters:
+ # Apply gross check using pccf
+ # Step 0-A: Create Diagnostic Flags
+ # Diagnostic flag for pccf
+ - filter: Create Diagnostic Flags
+ filter variables:
+ - name: bendingAngle
+ flags:
+ - name: pccfCheckReject
+ initial value: false
+ force reinitialization: true
+
+ # Step 0-B: pccf Check for CDACC data - good: 0.1-100, reject: 0
+ - filter: Bounds Check
+ filter variables:
+ - name: bendingAngle
+ where:
+ - variable:
+ name: MetaData/satelliteIdentifier
+ is_in: 265-269,750-755,44,786,820,825
+ test variables:
+ - name: MetaData/pccf
+ minvalue: 0.1
+ maxvalue: 100.1
+ actions:
+ - name: set
+ flag: pccfCheckReject
+ - name: reject
+
+ #1. gpstop
+ - filter: Domain Check
+ filter variables:
+ - name: bendingAngle
+ where:
+ - variable:
+ name: MetaData/impactHeightRO
+ minvalue: 0
+ maxvalue: 55000.1
+ action:
+ name: reject
+ #3. RONBAM cut off check
+ - filter: Background Check RONBAM
+ filter variables:
+ - name: bendingAngle
+ action:
+ name: reject
+ defer to post: true
+ #4. assign obs error
+ - filter: ROobserror
+ filter variables:
+ - name: bendingAngle
+ errmodel: NBAM
+ defer to post: true
+ #5. Obs error inflate
+ - filter: Perform Action
+ filter variables:
+ - name: bendingAngle
+ action:
+ name: RONBAMErrInflate
+ defer to post: true
+ # --------------------------------
diff --git a/parm/jcb-gdas/observations/atmosphere/gnssro_grace.yaml.j2 b/parm/jcb-gdas/observations/atmosphere/gnssro_grace.yaml.j2
new file mode 100644
index 000000000..5e77ca283
--- /dev/null
+++ b/parm/jcb-gdas/observations/atmosphere/gnssro_grace.yaml.j2
@@ -0,0 +1,95 @@
+-
+
+ # Observation Space (I/O)
+ # -----------------------
+ obs space:
+ name: {{observation_from_jcb}}
+ obsdatain:
+ engine:
+ type: H5File
+ obsfile: "{{atmosphere_obsdatain_path}}/{{atmosphere_obsdatain_prefix}}{{observation_from_jcb}}{{atmosphere_obsdatain_suffix}}"
+ missing file action: warn
+ obsgrouping:
+ group variables: [ 'sequenceNumber' ]
+ sort variable: 'impactHeightRO'
+ sort order: 'ascending'
+ obsdataout:
+ engine:
+ type: H5File
+ obsfile: "{{atmosphere_obsdataout_path}}/{{atmosphere_obsdataout_prefix}}{{observation_from_jcb}}{{atmosphere_obsdataout_suffix}}"
+ simulated variables: [bendingAngle]
+
+ # Observation Operator
+ # --------------------
+ obs operator:
+ name: GnssroBndNBAM
+ obs options:
+ use_compress: 1
+ sr_steps: 2
+ vertlayer: full
+ super_ref_qc: NBAM
+ output_diags: true
+
+ # Observation Filters (QC)
+ # ------------------------
+ obs filters:
+ # Apply gross check using pccf
+ # Step 0-A: Create Diagnostic Flags
+ # Diagnostic flag for pccf
+ - filter: Create Diagnostic Flags
+ filter variables:
+ - name: bendingAngle
+ flags:
+ - name: pccfCheckReject
+ initial value: false
+ force reinitialization: true
+
+ # Step 0-B: pccf Check for CDACC data - good: 0.1-100, reject: 0
+ - filter: Bounds Check
+ filter variables:
+ - name: bendingAngle
+ where:
+ - variable:
+ name: MetaData/satelliteIdentifier
+ is_in: 265-269,750-755,44,786,820,825
+ test variables:
+ - name: MetaData/pccf
+ minvalue: 0.1
+ maxvalue: 100.1
+ actions:
+ - name: set
+ flag: pccfCheckReject
+ - name: reject
+
+ #1. gpstop
+ - filter: Domain Check
+ filter variables:
+ - name: bendingAngle
+ where:
+ - variable:
+ name: MetaData/impactHeightRO
+ minvalue: 0
+ maxvalue: 55000.1
+ action:
+ name: reject
+ #3. RONBAM cut off check
+ - filter: Background Check RONBAM
+ filter variables:
+ - name: bendingAngle
+ action:
+ name: reject
+ defer to post: true
+ #4. assign obs error
+ - filter: ROobserror
+ filter variables:
+ - name: bendingAngle
+ errmodel: NBAM
+ defer to post: true
+ #5. Obs error inflate
+ - filter: Perform Action
+ filter variables:
+ - name: bendingAngle
+ action:
+ name: RONBAMErrInflate
+ defer to post: true
+ # --------------------------------
diff --git a/parm/jcb-gdas/observations/atmosphere/gnssro_metop.yaml.j2 b/parm/jcb-gdas/observations/atmosphere/gnssro_metop.yaml.j2
new file mode 100644
index 000000000..a3754e23d
--- /dev/null
+++ b/parm/jcb-gdas/observations/atmosphere/gnssro_metop.yaml.j2
@@ -0,0 +1,108 @@
+-
+
+ # Observation Space (I/O)
+ # -----------------------
+ obs space:
+ name: {{observation_from_jcb}}
+ obsdatain:
+ engine:
+ type: H5File
+ obsfile: "{{atmosphere_obsdatain_path}}/{{atmosphere_obsdatain_prefix}}{{observation_from_jcb}}{{atmosphere_obsdatain_suffix}}"
+ missing file action: warn
+ obsgrouping:
+ group variables: [ 'sequenceNumber' ]
+ sort variable: 'impactHeightRO'
+ sort order: 'ascending'
+ obsdataout:
+ engine:
+ type: H5File
+ obsfile: "{{atmosphere_obsdataout_path}}/{{atmosphere_obsdataout_prefix}}{{observation_from_jcb}}{{atmosphere_obsdataout_suffix}}"
+ simulated variables: [bendingAngle]
+
+ # Observation Operator
+ # --------------------
+ obs operator:
+ name: GnssroBndNBAM
+ obs options:
+ use_compress: 1
+ sr_steps: 2
+ vertlayer: full
+ super_ref_qc: NBAM
+ output_diags: true
+
+ # Observation Filters (QC)
+ # ------------------------
+ obs filters:
+ # Apply gross check using qfro
+ # Step 0-A: Create Diagnostic Flags
+ # Diagnostic flag for qfro
+ - filter: Create Diagnostic Flags
+ filter variables:
+ - name: bendingAngle
+ flags:
+ - name: qfroCheckReject
+ initial value: false
+ force reinitialization: true
+
+ # Step 0-B: qfro Check - good: 0, reject: 1
+ - filter: Bounds Check
+ filter variables:
+ - name: bendingAngle
+ where:
+ - variable:
+ name: MetaData/satelliteIdentifier
+ is_in: 3-5,421,440,821
+ test variables:
+ - name: MetaData/qualityFlags
+ minvalue: -0.1
+ maxvalue: 0.9
+ actions:
+ - name: set
+ flag: qfroCheckReject
+ - name: reject
+
+ #1. gpstop
+ - filter: Domain Check
+ filter variables:
+ - name: bendingAngle
+ where:
+ - variable:
+ name: MetaData/impactHeightRO
+ minvalue: 0
+ maxvalue: 55000.1
+ action:
+ name: reject
+ #2. metop below 8 km
+ - filter: Bounds Check
+ filter variables:
+ - name: bendingAngle
+ where:
+ - variable:
+ name: MetaData/satelliteIdentifier
+ is_in: 3-5
+ test variables:
+ - name: MetaData/impactHeightRO
+ minvalue: 8000.1
+ action:
+ name: reject
+ #3. RONBAM cut off check
+ - filter: Background Check RONBAM
+ filter variables:
+ - name: bendingAngle
+ action:
+ name: reject
+ defer to post: true
+ #4. assign obs error
+ - filter: ROobserror
+ filter variables:
+ - name: bendingAngle
+ errmodel: NBAM
+ defer to post: true
+ #5. Obs error inflate
+ - filter: Perform Action
+ filter variables:
+ - name: bendingAngle
+ action:
+ name: RONBAMErrInflate
+ defer to post: true
+ # --------------------------------
diff --git a/parm/jcb-gdas/observations/atmosphere/gnssro_paz.yaml.j2 b/parm/jcb-gdas/observations/atmosphere/gnssro_paz.yaml.j2
new file mode 100644
index 000000000..366df08e2
--- /dev/null
+++ b/parm/jcb-gdas/observations/atmosphere/gnssro_paz.yaml.j2
@@ -0,0 +1,95 @@
+-
+
+ # Observation Space (I/O)
+ # -----------------------
+ obs space:
+ name: {{observation_from_jcb}}
+ obsdatain:
+ engine:
+ type: H5File
+ obsfile: "{{atmosphere_obsdatain_path}}/{{atmosphere_obsdatain_prefix}}{{observation_from_jcb}}{{atmosphere_obsdatain_suffix}}"
+ missing file action: warn
+ obsgrouping:
+ group variables: [ 'sequenceNumber' ]
+ sort variable: 'impactHeightRO'
+ sort order: 'ascending'
+ obsdataout:
+ engine:
+ type: H5File
+ obsfile: "{{atmosphere_obsdataout_path}}/{{atmosphere_obsdataout_prefix}}{{observation_from_jcb}}{{atmosphere_obsdataout_suffix}}"
+ simulated variables: [bendingAngle]
+
+ # Observation Operator
+ # --------------------
+ obs operator:
+ name: GnssroBndNBAM
+ obs options:
+ use_compress: 1
+ sr_steps: 2
+ vertlayer: full
+ super_ref_qc: NBAM
+ output_diags: true
+
+ # Observation Filters (QC)
+ # ------------------------
+ obs filters:
+ # Apply gross check using pccf
+ # Step 0-A: Create Diagnostic Flags
+ # Diagnostic flag for pccf
+ - filter: Create Diagnostic Flags
+ filter variables:
+ - name: bendingAngle
+ flags:
+ - name: pccfCheckReject
+ initial value: false
+ force reinitialization: true
+
+ # Step 0-B: pccf Check for CDACC data - good: 0.1-100, reject: 0
+ - filter: Bounds Check
+ filter variables:
+ - name: bendingAngle
+ where:
+ - variable:
+ name: MetaData/satelliteIdentifier
+ is_in: 265-269,750-755,44,786,820,825
+ test variables:
+ - name: MetaData/pccf
+ minvalue: 0.1
+ maxvalue: 100.1
+ actions:
+ - name: set
+ flag: pccfCheckReject
+ - name: reject
+
+ #1. gpstop
+ - filter: Domain Check
+ filter variables:
+ - name: bendingAngle
+ where:
+ - variable:
+ name: MetaData/impactHeightRO
+ minvalue: 0
+ maxvalue: 55000.1
+ action:
+ name: reject
+ #3. RONBAM cut off check
+ - filter: Background Check RONBAM
+ filter variables:
+ - name: bendingAngle
+ action:
+ name: reject
+ defer to post: true
+ #4. assign obs error
+ - filter: ROobserror
+ filter variables:
+ - name: bendingAngle
+ errmodel: NBAM
+ defer to post: true
+ #5. Obs error inflate
+ - filter: Perform Action
+ filter variables:
+ - name: bendingAngle
+ action:
+ name: RONBAMErrInflate
+ defer to post: true
+ # --------------------------------
diff --git a/parm/jcb-gdas/observations/atmosphere/gnssro_spire.yaml.j2 b/parm/jcb-gdas/observations/atmosphere/gnssro_spire.yaml.j2
new file mode 100644
index 000000000..bc4988048
--- /dev/null
+++ b/parm/jcb-gdas/observations/atmosphere/gnssro_spire.yaml.j2
@@ -0,0 +1,97 @@
+-
+
+ # Observation Space (I/O)
+ # -----------------------
+ obs space:
+ name: {{observation_from_jcb}}
+ obsdatain:
+ engine:
+ type: H5File
+ obsfile: "{{atmosphere_obsdatain_path}}/{{atmosphere_obsdatain_prefix}}{{observation_from_jcb}}{{atmosphere_obsdatain_suffix}}"
+ missing file action: warn
+ obsgrouping:
+ group variables: [ 'sequenceNumber' ]
+ sort variable: 'impactHeightRO'
+ sort order: 'ascending'
+ obsdataout:
+ engine:
+ type: H5File
+ obsfile: "{{atmosphere_obsdataout_path}}/{{atmosphere_obsdataout_prefix}}{{observation_from_jcb}}{{atmosphere_obsdataout_suffix}}"
+ simulated variables: [bendingAngle]
+
+ # Observation Operator
+ # --------------------
+ obs operator:
+ name: GnssroBndNBAM
+ obs options:
+ use_compress: 1
+ sr_steps: 2
+ vertlayer: full
+ super_ref_qc: NBAM
+ output_diags: true
+
+ # Observation Filters (QC)
+ # ------------------------
+ obs filters:
+ # Apply gross check using pccf
+ # Step 0-A: Create Diagnostic Flags
+ # Diagnostic flag for pccf
+ - filter: Create Diagnostic Flags
+ filter variables:
+ - name: bendingAngle
+ flags:
+ - name: pccfCheckReject
+ initial value: false
+ force reinitialization: true
+
+ # Step 0-B: pccf Check for CDACC data - good: 0.1-100, reject: 0
+ - filter: Bounds Check
+ filter variables:
+ - name: bendingAngle
+ where:
+ - variable:
+ name: MetaData/satelliteIdentifier
+ is_in: 265-269,750-755,44,786,820,825
+ test variables:
+ - name: MetaData/pccf
+ minvalue: 0.1
+ maxvalue: 100.1
+ actions:
+ - name: set
+ flag: pccfCheckReject
+ - name: reject
+
+ #1. commgpstop
+ - filter: Bounds Check
+ filter variables:
+ - name: bendingAngle
+ where:
+ - variable:
+ name: MetaData/satelliteIdentifier
+ is_in: 265,266,267,268,269
+ test variables:
+ - name: MetaData/impactHeightRO
+ maxvalue: 45000.1
+ action:
+ name: reject
+ #3. RONBAM cut off check
+ - filter: Background Check RONBAM
+ filter variables:
+ - name: bendingAngle
+ action:
+ name: reject
+ defer to post: true
+ #4. assign obs error
+ - filter: ROobserror
+ filter variables:
+ - name: bendingAngle
+ errmodel: NBAM
+ defer to post: true
+ #5. Obs error inflate
+ - filter: Perform Action
+ filter variables:
+ - name: bendingAngle
+ action:
+ name: RONBAMErrInflate
+ defer to post: true
+ # --------------------------------
diff --git a/parm/jcb-gdas/observations/atmosphere/prepbufr_adpsfc.yaml.j2 b/parm/jcb-gdas/observations/atmosphere/prepbufr_adpsfc.yaml.j2
new file mode 100644
index 000000000..d11297ebf
--- /dev/null
+++ b/parm/jcb-gdas/observations/atmosphere/prepbufr_adpsfc.yaml.j2
@@ -0,0 +1,369 @@
+-
+
+ # Observation Space (I/O)
+ # -----------------------
+ obs space:
+ name: {{observation_from_jcb}}
+ obsdatain:
+ engine:
+ type: H5File
+ obsfile: "{{atmosphere_obsdatain_path}}/{{atmosphere_obsdatain_prefix}}{{observation_from_jcb}}{{atmosphere_obsdatain_suffix}}"
+ missing file action: warn
+ obsdataout:
+ engine:
+ type: H5File
+ obsfile: "{{atmosphere_obsdataout_path}}/{{atmosphere_obsdataout_prefix}}{{observation_from_jcb}}{{atmosphere_obsdataout_suffix}}"
+ io pool:
+ max pool size: 1
+ simulated variables: [stationPressure]
+
+ # Observation Operator
+ # --------------------
+ obs operator:
+ name: SfcCorrected
+ variables:
+ - name: stationPressure
+ correction scheme to use: GSL
+ station_altitude: height
+ geovar_sfc_geomz: height_above_mean_sea_level_at_surface
+ geovar_geomz: geopotential_height
+
+ # Linear Observation Operator
+ # ---------------------------
+ linear obs operator:
+ name: Identity
+ variables:
+ - name: stationPressure
+
+ # Observation Prior Filters (QC)
+ # ------------------------------
+ obs prior filters:
+ # Initial Error Assignments for SFC Observations
+ - filter: Perform Action
+ filter variables:
+ - name: stationPressure
+ where:
+ - variable: ObsType/stationPressure
+ is_in: [181]
+ action:
+ name: assign error
+ error function:
+ name: ObsFunction/ObsErrorModelStepwiseLinear
+ options:
+ round_to_the_nearest_integer: true
+ xvar:
+ name: ObsValue/stationPressure
+ xvals: [80000, 75000, 70000, 65000, 60000, 55000]
+ errors: [110, 120, 120, 120, 120, 1.0e+11]
+
+ - filter: Perform Action
+ filter variables:
+ - name: stationPressure
+ where:
+ - variable: ObsType/stationPressure
+ is_in: [187]
+ action:
+ name: assign error
+ error function:
+ name: ObsFunction/ObsErrorModelStepwiseLinear
+ options:
+ round_to_the_nearest_integer: true
+ xvar:
+ name: ObsValue/stationPressure
+ xvals: [85000, 80000, 75000, 70000, 65000, 60000, 55000]
+ errors: [120, 140, 140, 140, 140, 140, 1.0e+11]
+
+ # Initial Error Assignments for SFCSHIP Observations
+ - filter: Perform Action
+ filter variables:
+ - name: stationPressure
+ where:
+ - variable: ObsType/stationPressure
+ is_in: [180]
+ action:
+ name: assign error
+ error function:
+ name: ObsFunction/ObsErrorModelStepwiseLinear
+ options:
+ round_to_the_nearest_integer: true
+ xvar:
+ name: ObsValue/stationPressure
+ xvals: [60000, 55000]
+ errors: [130, 1.0e+11]
+
+ - filter: Perform Action
+ filter variables:
+ - name: stationPressure
+ where:
+ - variable: ObsType/stationPressure
+ is_in: [183]
+ action:
+ name: assign error
+ error parameter: 1.0e+11
+
+ # Initial Error Assignments for Radiosonde
+ - filter: Perform Action
+ filter variables:
+ - name: stationPressure
+ where:
+ - variable: ObsType/stationPressure
+ is_in: [120]
+ action:
+ name: assign error
+ error function:
+ name: ObsFunction/ObsErrorModelStepwiseLinear
+ options:
+ round_to_the_nearest_integer: true
+ xvar:
+ name: ObsValue/stationPressure
+ xvals: [80000, 75000, 70000, 65000, 60000, 55000]
+ errors: [110, 120, 120, 120, 120, 1.0e+11]
+
+ # Create PreQC group variable (pqm in GSI read_prepbufr)
+ - filter: Variable Assignment
+ assignments:
+ - name: InputObsError/stationPressure
+ type: float
+ source variable: ObsErrorData/stationPressure
+
+ # Set observation quality-realted variables
+ # Create PreQC group variable (pqm in GSI read_prepbufr)
+ - filter: Variable Assignment
+ assignments:
+ - name: PreQC/stationPressure
+ type: int
+ source variable: QualityMarker/stationPressure
+
+ # Create PreUseFlag group variable (usage in GSI read_prepbufr)
+ # Initialize
+ - filter: Variable Assignment
+ assignments:
+ - name: PreUseFlag/stationPressure
+ type: int
+ source variable: PreQC/stationPressure
+
+ - filter: Variable Assignment
+ where:
+ - variable:
+ name: PreUseFlag/stationPressure
+ is_in: 1-15
+ assignments:
+ - name: PreUseFlag/stationPressure
+ value: 0
+ # Re-assignment
+ - filter: Variable Assignment
+ where:
+ - variable:
+ name: ObsType/stationPressure
+ is_in: 183
+ assignments:
+ - name: PreUseFlag/stationPressure
+ value: 100
+
+ - filter: Variable Assignment
+ where:
+ - variable:
+ name: ObsValue/stationPressure
+ is_defined:
+ - variable:
+ name: ObsValue/stationPressure
+ maxvalue: 50000.00
+ where operator: and
+ assignments:
+ - name: PreUseFlag/stationPressure
+ value: 100
+
+ - filter: Variable Assignment
+ where:
+ - variable:
+ name: PreQC/stationPressure
+ is_in: 9, 12, 15
+ assignments:
+ - name: PreUseFlag/stationPressure
+ value: 100
+
+ - filter: Variable Assignment
+ where:
+ - variable:
+ name: PreQC/stationPressure
+ is_in: 4-15
+ assignments:
+ - name: PreUseFlag/stationPressure
+ value: 101
+
+ ## Observation range sanity check
+ #- filter: Bounds Check
+ # filter variables:
+ # - name: stationPressure
+ # minvalue: 37499.0
+ # maxvalue: 106999.0
+ # action:
+ # name: reject
+ ## Reject all ObsType 183
+ #- filter: RejectList
+ # where:
+ # - variable:
+ # name: ObsType/stationPressure
+ # is_in: 183
+ ## Reject surface pressure below 500 hPa
+ #- filter: Bounds Check
+ # filter variables:
+ # - name: stationPressure
+ # minvalue: 50000.00
+ # action:
+ # name: reject
+ #- filter: RejectList
+ # where:
+ # - variable:
+ # name: PreQC/stationPressure
+ # is_in: 4-15
+ # Inflate obs error based on obs type
+ - filter: Perform Action
+ filter variables:
+ - name: stationPressure
+ where:
+ - variable: PreQC/stationPressure
+ is_in: 3, 7
+ action:
+ name: inflate error
+ inflation factor: 1.2
+
+ # Observation Post Filters (QC)
+ # -----------------------------
+ obs post filters:
+ # Calculate obs error inflation factors for duplicated observations at the same location
+ - filter: Variable Assignment
+ assignments:
+ - name: ObsErrorFactorDuplicateCheck/stationPressure
+ type: float
+ function:
+ name: ObsFunction/ObsErrorFactorDuplicateCheck
+ options:
+ use_air_pressure: false
+ variable: stationPressure
+
+ # Reduce effective observation error based on obs type and subtype
+ # In this case: reduce effective obs error for buoy
+ - filter: Perform Action
+ filter variables:
+ - name: stationPressure
+ where:
+ - variable:
+ name: ObsType/stationPressure
+ is_in: 180
+ - variable:
+ name: MetaData/observationSubTypeNum
+ is_in: 0
+ action:
+ name: inflate error
+ inflation factor: 0.7
+
+ # Calculate obs error inflation factors for large discrepancies between model and observations
+ - filter: Variable Assignment
+ assignments:
+ - name: ObsErrorFactorSfcPressure/stationPressure
+ type: float
+ function:
+ name: ObsFunction/ObsErrorFactorSfcPressure
+ options:
+ geovar_sfc_geomz: height_above_mean_sea_level_at_surface
+ geovar_geomz: geopotential_height
+ station_altitude: height
+
+ # Inflate surface pressure observation based on discrepancies between
+ # model and observations due to terrian
+ - filter: Perform Action
+ filter variables:
+ - name: stationPressure
+ action:
+ name: inflate error
+ inflation variable:
+ name: ObsErrorFactorSfcPressure/stationPressure
+
+ - filter: Variable Assignment
+ assignments:
+ - name: DerivedMetaData/Innovation
+ type: float
+ function:
+ name: ObsFunction/Arithmetic
+ options:
+ variables:
+ - name: ObsValue/stationPressure
+ - name: HofX/stationPressure
+ coefs: [1, -1]
+
+ - filter: Variable Assignment
+ assignments:
+ - name: DerivedMetaData/ObsErrorBoundSfcPressure1
+ type: float
+ function:
+ name: ObsFunction/ObsErrorBoundConventional
+ options:
+ obsvar: stationPressure
+ obserr_bound_min: 100
+ obserr_bound_max: 300
+ obserr_bound_factor: 5.0
+
+ - filter: Background Check
+ filter variables:
+ - name: stationPressure
+ where:
+ - variable: PreQC/stationPressure
+ is_not_in: 3
+ function absolute threshold:
+ - name: DerivedMetaData/ObsErrorBoundSfcPressure1
+ action:
+ name: reject
+
+ - filter: Variable Assignment
+ assignments:
+ - name: DerivedMetaData/ObsErrorBoundSfcPressure2
+ type: float
+ function:
+ name: ObsFunction/ObsErrorBoundConventional
+ options:
+ obsvar: stationPressure
+ obserr_bound_min: 100
+ obserr_bound_max: 300
+ obserr_bound_factor: 3.5
+
+ - filter: Background Check
+ filter variables:
+ - name: stationPressure
+ where:
+ - variable: PreQC/stationPressure
+ is_in: 3
+ function absolute threshold:
+ - name: DerivedMetaData/ObsErrorBoundSfcPressure2
+ action:
+ name: reject
+
+ # Inflate obs error based on duplicate check
+ - filter: Perform Action
+ filter variables:
+ - name: stationPressure
+ action:
+ name: inflate error
+ inflation variable:
+ name: ObsErrorFactorDuplicateCheck/stationPressure
+
+ # Reject data based on PreUseFlag (usage in GSI)
+ - filter: Perform Action
+ filter variables:
+ - name: stationPressure
+ where:
+ - variable: PreUseFlag/stationPressure
+ is_not_in: 0, 1
+ action:
+ name: reject
+ # End of Filters
+
+
+ # GeoVaLs for Driving Observation Operators (testing mode)
+ # --------------------------------------------------------
+ geovals:
+ filename: "{{atmosphere_obsdatain_path}}/{{atmosphere_obsdatain_prefix}}{{observation_from_jcb}}_geoval{{atmosphere_obsdatain_suffix}}"
+
+ # Passed benchmark for UFO testing
+ # --------------------------------
+ passedBenchmark: 0
diff --git a/parm/jcb-gdas/observations/atmosphere/prepbufr_adpupa.yaml.j2 b/parm/jcb-gdas/observations/atmosphere/prepbufr_adpupa.yaml.j2
new file mode 100644
index 000000000..7d6c7190d
--- /dev/null
+++ b/parm/jcb-gdas/observations/atmosphere/prepbufr_adpupa.yaml.j2
@@ -0,0 +1,369 @@
+-
+
+ # Observation Space (I/O)
+ # -----------------------
+ obs space:
+ name: {{observation_from_jcb}}
+ obsdatain:
+ engine:
+ type: H5File
+ obsfile: "{{atmosphere_obsdatain_path}}/{{atmosphere_obsdatain_prefix}}{{observation_from_jcb}}{{atmosphere_obsdatain_suffix}}"
+ missing file action: warn
+ obsdataout:
+ engine:
+ type: H5File
+ obsfile: "{{atmosphere_obsdataout_path}}/{{atmosphere_obsdataout_prefix}}{{observation_from_jcb}}{{atmosphere_obsdataout_suffix}}"
+ io pool:
+ max pool size: 1
+ simulated variables: [stationPressure]
+
+ # Observation Operator
+ # --------------------
+ obs operator:
+ name: SfcCorrected
+ variables:
+ - name: stationPressure
+ correction scheme to use: GSL
+ station_altitude: height
+ geovar_sfc_geomz: height_above_mean_sea_level_at_surface
+ geovar_geomz: geopotential_height
+
+ # Linear Observation Operator
+ # ---------------------------
+ linear obs operator:
+ name: Identity
+ variables:
+ - name: stationPressure
+
+ # Observation Prior Filters (QC)
+ # ------------------------------
+ obs prior filters:
+ # Initial Error Assignments for SFC Observations
+ - filter: Perform Action
+ filter variables:
+ - name: stationPressure
+ where:
+ - variable: ObsType/pressure
+ is_in: [181]
+ action:
+ name: assign error
+ error function:
+ name: ObsFunction/ObsErrorModelStepwiseLinear
+ options:
+ round_to_the_nearest_integer: true
+ xvar:
+ name: ObsValue/stationPressure
+ xvals: [80000, 75000, 70000, 65000, 60000, 55000]
+ errors: [110, 120, 120, 120, 120, 1.0e+11]
+
+ - filter: Perform Action
+ filter variables:
+ - name: stationPressure
+ where:
+ - variable: ObsType/pressure
+ is_in: [187]
+ action:
+ name: assign error
+ error function:
+ name: ObsFunction/ObsErrorModelStepwiseLinear
+ options:
+ round_to_the_nearest_integer: true
+ xvar:
+ name: ObsValue/stationPressure
+ xvals: [85000, 80000, 75000, 70000, 65000, 60000, 55000]
+ errors: [120, 140, 140, 140, 140, 140, 1.0e+11]
+
+ # Initial Error Assignments for SFCSHIP Observations
+ - filter: Perform Action
+ filter variables:
+ - name: stationPressure
+ where:
+ - variable: ObsType/pressure
+ is_in: [180]
+ action:
+ name: assign error
+ error function:
+ name: ObsFunction/ObsErrorModelStepwiseLinear
+ options:
+ round_to_the_nearest_integer: true
+ xvar:
+ name: ObsValue/stationPressure
+ xvals: [60000, 55000]
+ errors: [130, 1.0e+11]
+
+ - filter: Perform Action
+ filter variables:
+ - name: stationPressure
+ where:
+ - variable: ObsType/pressure
+ is_in: [183]
+ action:
+ name: assign error
+ error parameter: 1.0e+11
+
+ # Initial Error Assignments for Radiosonde
+ - filter: Perform Action
+ filter variables:
+ - name: stationPressure
+ where:
+ - variable: ObsType/pressure
+ is_in: [120]
+ action:
+ name: assign error
+ error function:
+ name: ObsFunction/ObsErrorModelStepwiseLinear
+ options:
+ round_to_the_nearest_integer: true
+ xvar:
+ name: ObsValue/stationPressure
+ xvals: [80000, 75000, 70000, 65000, 60000, 55000]
+ errors: [110, 120, 120, 120, 120, 1.0e+11]
+
+ # Create PreQC group variable (pqm in GSI read_prepbufr)
+ - filter: Variable Assignment
+ assignments:
+ - name: InputObsError/stationPressure
+ type: float
+ source variable: ObsErrorData/stationPressure
+
+ # Set observation quality-realted variables
+ # Create PreQC group variable (pqm in GSI read_prepbufr)
+ - filter: Variable Assignment
+ assignments:
+ - name: PreQC/stationPressure
+ type: int
+ source variable: QualityMarker/stationPressure
+
+ # Create PreUseFlag group variable (usage in GSI read_prepbufr)
+ # Initialize
+ - filter: Variable Assignment
+ assignments:
+ - name: PreUseFlag/stationPressure
+ type: int
+ source variable: PreQC/stationPressure
+
+ - filter: Variable Assignment
+ where:
+ - variable:
+ name: PreUseFlag/stationPressure
+ is_in: 1-15
+ assignments:
+ - name: PreUseFlag/stationPressure
+ value: 0
+ # Re-assignment
+ - filter: Variable Assignment
+ where:
+ - variable:
+ name: ObsType/pressure
+ is_in: 183
+ assignments:
+ - name: PreUseFlag/stationPressure
+ value: 100
+
+ - filter: Variable Assignment
+ where:
+ - variable:
+ name: ObsValue/stationPressure
+ is_defined:
+ - variable:
+ name: ObsValue/stationPressure
+ maxvalue: 50000.00
+ where operator: and
+ assignments:
+ - name: PreUseFlag/stationPressure
+ value: 100
+
+ - filter: Variable Assignment
+ where:
+ - variable:
+ name: PreQC/stationPressure
+ is_in: 9, 12, 15
+ assignments:
+ - name: PreUseFlag/stationPressure
+ value: 100
+
+ - filter: Variable Assignment
+ where:
+ - variable:
+ name: PreQC/stationPressure
+ is_in: 4-15
+ assignments:
+ - name: PreUseFlag/stationPressure
+ value: 101
+
+ ## Observation range sanity check
+ #- filter: Bounds Check
+ # filter variables:
+ # - name: stationPressure
+ # minvalue: 37499.0
+ # maxvalue: 106999.0
+ # action:
+ # name: reject
+ ## Reject all ObsType 183
+ #- filter: RejectList
+ # where:
+ # - variable:
+ # name: ObsType/pressure
+ # is_in: 183
+ ## Reject surface pressure below 500 hPa
+ #- filter: Bounds Check
+ # filter variables:
+ # - name: stationPressure
+ # minvalue: 50000.00
+ # action:
+ # name: reject
+ #- filter: RejectList
+ # where:
+ # - variable:
+ # name: PreQC/stationPressure
+ # is_in: 4-15
+ # Inflate obs error based on obs type
+ - filter: Perform Action
+ filter variables:
+ - name: stationPressure
+ where:
+ - variable: PreQC/stationPressure
+ is_in: 3, 7
+ action:
+ name: inflate error
+ inflation factor: 1.2
+
+ # Observation Post Filters (QC)
+ # -----------------------------
+ obs post filters:
+ # Calculate obs error inflation factors for duplicated observations at the same location
+ - filter: Variable Assignment
+ assignments:
+ - name: ObsErrorFactorDuplicateCheck/stationPressure
+ type: float
+ function:
+ name: ObsFunction/ObsErrorFactorDuplicateCheck
+ options:
+ use_air_pressure: false
+ variable: stationPressure
+
+ # Reduce effective observation error based on obs type and subtype
+ # In this case: reduce effective obs error for buoy
+ - filter: Perform Action
+ filter variables:
+ - name: stationPressure
+ where:
+ - variable:
+ name: ObsType/pressure
+ is_in: 180
+ - variable:
+ name: ObsSubType/stationPressure
+ is_in: 0
+ action:
+ name: inflate error
+ inflation factor: 0.7
+
+ # Calculate obs error inflation factors for large discrepancies between model and observations
+ - filter: Variable Assignment
+ assignments:
+ - name: ObsErrorFactorSfcPressure/stationPressure
+ type: float
+ function:
+ name: ObsFunction/ObsErrorFactorSfcPressure
+ options:
+ geovar_sfc_geomz: height_above_mean_sea_level_at_surface
+ geovar_geomz: geopotential_height
+ station_altitude: height
+
+ # Inflate surface pressure observation based on discrepancies between
+ # model and observations due to terrian
+ - filter: Perform Action
+ filter variables:
+ - name: stationPressure
+ action:
+ name: inflate error
+ inflation variable:
+ name: ObsErrorFactorSfcPressure/stationPressure
+
+ - filter: Variable Assignment
+ assignments:
+ - name: DerivedMetaData/Innovation
+ type: float
+ function:
+ name: ObsFunction/Arithmetic
+ options:
+ variables:
+ - name: ObsValue/stationPressure
+ - name: HofX/stationPressure
+ coefs: [1, -1]
+
+ - filter: Variable Assignment
+ assignments:
+ - name: DerivedMetaData/ObsErrorBoundSfcPressure1
+ type: float
+ function:
+ name: ObsFunction/ObsErrorBoundConventional
+ options:
+ obsvar: stationPressure
+ obserr_bound_min: 100
+ obserr_bound_max: 300
+ obserr_bound_factor: 5.0
+
+ - filter: Background Check
+ filter variables:
+ - name: stationPressure
+ where:
+ - variable: PreQC/stationPressure
+ is_not_in: 3
+ function absolute threshold:
+ - name: DerivedMetaData/ObsErrorBoundSfcPressure1
+ action:
+ name: reject
+
+ - filter: Variable Assignment
+ assignments:
+ - name: DerivedMetaData/ObsErrorBoundSfcPressure2
+ type: float
+ function:
+ name: ObsFunction/ObsErrorBoundConventional
+ options:
+ obsvar: stationPressure
+ obserr_bound_min: 100
+ obserr_bound_max: 300
+ obserr_bound_factor: 3.5
+
+ - filter: Background Check
+ filter variables:
+ - name: stationPressure
+ where:
+ - variable: PreQC/stationPressure
+ is_in: 3
+ function absolute threshold:
+ - name: DerivedMetaData/ObsErrorBoundSfcPressure2
+ action:
+ name: reject
+
+ # Inflate obs error based on duplicate check
+ - filter: Perform Action
+ filter variables:
+ - name: stationPressure
+ action:
+ name: inflate error
+ inflation variable:
+ name: ObsErrorFactorDuplicateCheck/stationPressure
+
+ # Reject data based on PreUseFlag (usage in GSI)
+ - filter: Perform Action
+ filter variables:
+ - name: stationPressure
+ where:
+ - variable: PreUseFlag/stationPressure
+ is_not_in: 0, 1
+ action:
+ name: reject
+ # End of Filters
+
+
+ # GeoVaLs for Driving Observation Operators (testing mode)
+ # --------------------------------------------------------
+ geovals:
+ filename: "{{atmosphere_obsdatain_path}}/{{atmosphere_obsdatain_prefix}}{{observation_from_jcb}}_geoval{{atmosphere_obsdatain_suffix}}"
+
+ # Passed benchmark for UFO testing
+ # --------------------------------
+ passedBenchmark: 0
diff --git a/parm/jcb-gdas/observations/atmosphere/prepbufr_sfcshp.yaml.j2 b/parm/jcb-gdas/observations/atmosphere/prepbufr_sfcshp.yaml.j2
new file mode 100644
index 000000000..d11297ebf
--- /dev/null
+++ b/parm/jcb-gdas/observations/atmosphere/prepbufr_sfcshp.yaml.j2
@@ -0,0 +1,369 @@
+-
+
+ # Observation Space (I/O)
+ # -----------------------
+ obs space:
+ name: {{observation_from_jcb}}
+ obsdatain:
+ engine:
+ type: H5File
+ obsfile: "{{atmosphere_obsdatain_path}}/{{atmosphere_obsdatain_prefix}}{{observation_from_jcb}}{{atmosphere_obsdatain_suffix}}"
+ missing file action: warn
+ obsdataout:
+ engine:
+ type: H5File
+ obsfile: "{{atmosphere_obsdataout_path}}/{{atmosphere_obsdataout_prefix}}{{observation_from_jcb}}{{atmosphere_obsdataout_suffix}}"
+ io pool:
+ max pool size: 1
+ simulated variables: [stationPressure]
+
+ # Observation Operator
+ # --------------------
+ obs operator:
+ name: SfcCorrected
+ variables:
+ - name: stationPressure
+ correction scheme to use: GSL
+ station_altitude: height
+ geovar_sfc_geomz: height_above_mean_sea_level_at_surface
+ geovar_geomz: geopotential_height
+
+ # Linear Observation Operator
+ # ---------------------------
+ linear obs operator:
+ name: Identity
+ variables:
+ - name: stationPressure
+
+ # Observation Prior Filters (QC)
+ # ------------------------------
+ obs prior filters:
+ # Initial Error Assignments for SFC Observations
+ - filter: Perform Action
+ filter variables:
+ - name: stationPressure
+ where:
+ - variable: ObsType/stationPressure
+ is_in: [181]
+ action:
+ name: assign error
+ error function:
+ name: ObsFunction/ObsErrorModelStepwiseLinear
+ options:
+ round_to_the_nearest_integer: true
+ xvar:
+ name: ObsValue/stationPressure
+ xvals: [80000, 75000, 70000, 65000, 60000, 55000]
+ errors: [110, 120, 120, 120, 120, 1.0e+11]
+
+ - filter: Perform Action
+ filter variables:
+ - name: stationPressure
+ where:
+ - variable: ObsType/stationPressure
+ is_in: [187]
+ action:
+ name: assign error
+ error function:
+ name: ObsFunction/ObsErrorModelStepwiseLinear
+ options:
+ round_to_the_nearest_integer: true
+ xvar:
+ name: ObsValue/stationPressure
+ xvals: [85000, 80000, 75000, 70000, 65000, 60000, 55000]
+ errors: [120, 140, 140, 140, 140, 140, 1.0e+11]
+
+ # Initial Error Assignments for SFCSHIP Observations
+ - filter: Perform Action
+ filter variables:
+ - name: stationPressure
+ where:
+ - variable: ObsType/stationPressure
+ is_in: [180]
+ action:
+ name: assign error
+ error function:
+ name: ObsFunction/ObsErrorModelStepwiseLinear
+ options:
+ round_to_the_nearest_integer: true
+ xvar:
+ name: ObsValue/stationPressure
+ xvals: [60000, 55000]
+ errors: [130, 1.0e+11]
+
+ - filter: Perform Action
+ filter variables:
+ - name: stationPressure
+ where:
+ - variable: ObsType/stationPressure
+ is_in: [183]
+ action:
+ name: assign error
+ error parameter: 1.0e+11
+
+ # Initial Error Assignments for Radiosonde
+ - filter: Perform Action
+ filter variables:
+ - name: stationPressure
+ where:
+ - variable: ObsType/stationPressure
+ is_in: [120]
+ action:
+ name: assign error
+ error function:
+ name: ObsFunction/ObsErrorModelStepwiseLinear
+ options:
+ round_to_the_nearest_integer: true
+ xvar:
+ name: ObsValue/stationPressure
+ xvals: [80000, 75000, 70000, 65000, 60000, 55000]
+ errors: [110, 120, 120, 120, 120, 1.0e+11]
+
+ # Create PreQC group variable (pqm in GSI read_prepbufr)
+ - filter: Variable Assignment
+ assignments:
+ - name: InputObsError/stationPressure
+ type: float
+ source variable: ObsErrorData/stationPressure
+
+ # Set observation quality-realted variables
+ # Create PreQC group variable (pqm in GSI read_prepbufr)
+ - filter: Variable Assignment
+ assignments:
+ - name: PreQC/stationPressure
+ type: int
+ source variable: QualityMarker/stationPressure
+
+ # Create PreUseFlag group variable (usage in GSI read_prepbufr)
+ # Initialize
+ - filter: Variable Assignment
+ assignments:
+ - name: PreUseFlag/stationPressure
+ type: int
+ source variable: PreQC/stationPressure
+
+ - filter: Variable Assignment
+ where:
+ - variable:
+ name: PreUseFlag/stationPressure
+ is_in: 1-15
+ assignments:
+ - name: PreUseFlag/stationPressure
+ value: 0
+ # Re-assignment
+ - filter: Variable Assignment
+ where:
+ - variable:
+ name: ObsType/stationPressure
+ is_in: 183
+ assignments:
+ - name: PreUseFlag/stationPressure
+ value: 100
+
+ - filter: Variable Assignment
+ where:
+ - variable:
+ name: ObsValue/stationPressure
+ is_defined:
+ - variable:
+ name: ObsValue/stationPressure
+ maxvalue: 50000.00
+ where operator: and
+ assignments:
+ - name: PreUseFlag/stationPressure
+ value: 100
+
+ - filter: Variable Assignment
+ where:
+ - variable:
+ name: PreQC/stationPressure
+ is_in: 9, 12, 15
+ assignments:
+ - name: PreUseFlag/stationPressure
+ value: 100
+
+ - filter: Variable Assignment
+ where:
+ - variable:
+ name: PreQC/stationPressure
+ is_in: 4-15
+ assignments:
+ - name: PreUseFlag/stationPressure
+ value: 101
+
+ ## Observation range sanity check
+ #- filter: Bounds Check
+ # filter variables:
+ # - name: stationPressure
+ # minvalue: 37499.0
+ # maxvalue: 106999.0
+ # action:
+ # name: reject
+ ## Reject all ObsType 183
+ #- filter: RejectList
+ # where:
+ # - variable:
+ # name: ObsType/stationPressure
+ # is_in: 183
+ ## Reject surface pressure below 500 hPa
+ #- filter: Bounds Check
+ # filter variables:
+ # - name: stationPressure
+ # minvalue: 50000.00
+ # action:
+ # name: reject
+ #- filter: RejectList
+ # where:
+ # - variable:
+ # name: PreQC/stationPressure
+ # is_in: 4-15
+ # Inflate obs error based on obs type
+ - filter: Perform Action
+ filter variables:
+ - name: stationPressure
+ where:
+ - variable: PreQC/stationPressure
+ is_in: 3, 7
+ action:
+ name: inflate error
+ inflation factor: 1.2
+
+ # Observation Post Filters (QC)
+ # -----------------------------
+ obs post filters:
+ # Calculate obs error inflation factors for duplicated observations at the same location
+ - filter: Variable Assignment
+ assignments:
+ - name: ObsErrorFactorDuplicateCheck/stationPressure
+ type: float
+ function:
+ name: ObsFunction/ObsErrorFactorDuplicateCheck
+ options:
+ use_air_pressure: false
+ variable: stationPressure
+
+ # Reduce effective observation error based on obs type and subtype
+ # In this case: reduce effective obs error for buoy
+ - filter: Perform Action
+ filter variables:
+ - name: stationPressure
+ where:
+ - variable:
+ name: ObsType/stationPressure
+ is_in: 180
+ - variable:
+ name: MetaData/observationSubTypeNum
+ is_in: 0
+ action:
+ name: inflate error
+ inflation factor: 0.7
+
+ # Calculate obs error inflation factors for large discrepancies between model and observations
+ - filter: Variable Assignment
+ assignments:
+ - name: ObsErrorFactorSfcPressure/stationPressure
+ type: float
+ function:
+ name: ObsFunction/ObsErrorFactorSfcPressure
+ options:
+ geovar_sfc_geomz: height_above_mean_sea_level_at_surface
+ geovar_geomz: geopotential_height
+ station_altitude: height
+
+ # Inflate surface pressure observation based on discrepancies between
+ # model and observations due to terrian
+ - filter: Perform Action
+ filter variables:
+ - name: stationPressure
+ action:
+ name: inflate error
+ inflation variable:
+ name: ObsErrorFactorSfcPressure/stationPressure
+
+ - filter: Variable Assignment
+ assignments:
+ - name: DerivedMetaData/Innovation
+ type: float
+ function:
+ name: ObsFunction/Arithmetic
+ options:
+ variables:
+ - name: ObsValue/stationPressure
+ - name: HofX/stationPressure
+ coefs: [1, -1]
+
+ - filter: Variable Assignment
+ assignments:
+ - name: DerivedMetaData/ObsErrorBoundSfcPressure1
+ type: float
+ function:
+ name: ObsFunction/ObsErrorBoundConventional
+ options:
+ obsvar: stationPressure
+ obserr_bound_min: 100
+ obserr_bound_max: 300
+ obserr_bound_factor: 5.0
+
+ - filter: Background Check
+ filter variables:
+ - name: stationPressure
+ where:
+ - variable: PreQC/stationPressure
+ is_not_in: 3
+ function absolute threshold:
+ - name: DerivedMetaData/ObsErrorBoundSfcPressure1
+ action:
+ name: reject
+
+ - filter: Variable Assignment
+ assignments:
+ - name: DerivedMetaData/ObsErrorBoundSfcPressure2
+ type: float
+ function:
+ name: ObsFunction/ObsErrorBoundConventional
+ options:
+ obsvar: stationPressure
+ obserr_bound_min: 100
+ obserr_bound_max: 300
+ obserr_bound_factor: 3.5
+
+ - filter: Background Check
+ filter variables:
+ - name: stationPressure
+ where:
+ - variable: PreQC/stationPressure
+ is_in: 3
+ function absolute threshold:
+ - name: DerivedMetaData/ObsErrorBoundSfcPressure2
+ action:
+ name: reject
+
+ # Inflate obs error based on duplicate check
+ - filter: Perform Action
+ filter variables:
+ - name: stationPressure
+ action:
+ name: inflate error
+ inflation variable:
+ name: ObsErrorFactorDuplicateCheck/stationPressure
+
+ # Reject data based on PreUseFlag (usage in GSI)
+ - filter: Perform Action
+ filter variables:
+ - name: stationPressure
+ where:
+ - variable: PreUseFlag/stationPressure
+ is_not_in: 0, 1
+ action:
+ name: reject
+ # End of Filters
+
+
+ # GeoVaLs for Driving Observation Operators (testing mode)
+ # --------------------------------------------------------
+ geovals:
+ filename: "{{atmosphere_obsdatain_path}}/{{atmosphere_obsdatain_prefix}}{{observation_from_jcb}}_geoval{{atmosphere_obsdatain_suffix}}"
+
+ # Passed benchmark for UFO testing
+ # --------------------------------
+ passedBenchmark: 0
diff --git a/parm/jcb-gdas/observations/atmosphere/sfc.yaml.j2 b/parm/jcb-gdas/observations/atmosphere/sfc.yaml.j2
new file mode 100644
index 000000000..71ab0308d
--- /dev/null
+++ b/parm/jcb-gdas/observations/atmosphere/sfc.yaml.j2
@@ -0,0 +1,44 @@
+-
+
+ # Observation Space (I/O)
+ # -----------------------
+ obs space:
+ name: {{observation_from_jcb}}
+ obsdatain:
+ engine:
+ type: H5File
+ obsfile: "{{atmosphere_obsdatain_path}}/{{atmosphere_obsdatain_prefix}}{{observation_from_jcb}}{{atmosphere_obsdatain_suffix}}"
+ missing file action: warn
+ obsdataout:
+ engine:
+ type: H5File
+ obsfile: "{{atmosphere_obsdataout_path}}/{{atmosphere_obsdataout_prefix}}{{observation_from_jcb}}{{atmosphere_obsdataout_suffix}}"
+ io pool:
+ max pool size: 1
+ simulated variables: [stationPressure]
+
+ # Observation Operator
+ # --------------------
+ obs operator:
+ name: SfcCorrected
+ variables:
+ - name: stationPressure
+ correction scheme to use: GSL
+ station_altitude: height
+ geovar_sfc_geomz: height_above_mean_sea_level_at_surface
+ geovar_geomz: geopotential_height
+
+ # Linear Observation Operator
+ # ---------------------------
+ linear obs operator:
+ name: Identity
+
+
+ # GeoVaLs for Driving Observation Operators (testing mode)
+ # --------------------------------------------------------
+ geovals:
+ filename: "{{atmosphere_obsdatain_path}}/{{atmosphere_obsdatain_prefix}}{{observation_from_jcb}}_geoval{{atmosphere_obsdatain_suffix}}"
+
+ # Passed benchmark for UFO testing
+ # --------------------------------
+ passedBenchmark: 0
diff --git a/parm/jcb-gdas/observations/atmosphere/sfcship.yaml.j2 b/parm/jcb-gdas/observations/atmosphere/sfcship.yaml.j2
new file mode 100644
index 000000000..c0bc9e8c7
--- /dev/null
+++ b/parm/jcb-gdas/observations/atmosphere/sfcship.yaml.j2
@@ -0,0 +1,101 @@
+-
+
+ # Observation Space (I/O)
+ # -----------------------
+ obs space:
+ name: {{observation_from_jcb}}
+ obsdatain:
+ engine:
+ type: H5File
+ obsfile: "{{atmosphere_obsdatain_path}}/{{atmosphere_obsdatain_prefix}}{{observation_from_jcb}}{{atmosphere_obsdatain_suffix}}"
+ missing file action: warn
+ obsdataout:
+ engine:
+ type: H5File
+ overwrite: true
+ obsfile: "{{atmosphere_obsdataout_path}}/{{atmosphere_obsdataout_prefix}}{{observation_from_jcb}}{{atmosphere_obsdataout_suffix}}"
+ io pool:
+ max pool size: 1
+ simulated variables: [stationPressure, airTemperature, specificHumidity]
+
+ # Observation Operator
+ # --------------------
+ obs operator:
+ name: Composite
+ components:
+ - name: VertInterp
+ variables:
+ - name: airTemperature
+ - name: specificHumidity
+ - name: SfcCorrected
+ variables:
+ - name: stationPressure
+ correction scheme to use: GSL
+ geovar_sfc_geomz: height_above_mean_sea_level_at_surface
+ geovar_geomz: geopotential_height
+
+ # Linear Observation Operator
+ # ---------------------------
+ linear obs operator:
+ name: Identity
+
+ # Observation Filters (QC)
+ # ------------------------
+ obs filters:
+ # Observation range sanity check
+ - filter: Bounds Check
+ filter variables:
+ - name: stationPressure
+ minvalue: 37499.0
+ maxvalue: 106999.0
+ action:
+ name: reject
+ - filter: Bounds Check
+ filter variables:
+ - name: airTemperature
+ minvalue: 195.0
+ maxvalue: 327.0
+ action:
+ name: reject
+ - filter: Bounds Check
+ filter variables:
+ - name: specificHumidity
+ minvalue: 0.0
+ maxvalue: 0.03499
+ action:
+ name: reject
+
+ # Gross error check with (O - B) / ObsError greater than threshold.
+ - filter: Background Check
+ filter variables:
+ - name: stationPressure
+ threshold: 3.6
+ absolute threshold: 990.0
+ action:
+ name: reject
+ defer to post: true
+ - filter: Background Check
+ filter variables:
+ - name: airTemperature
+ threshold: 7.0
+ absolute threshold: 9.0
+ action:
+ name: reject
+ defer to post: true
+
+ # Reject all ObsType 183
+ - filter: BlackList
+ where:
+ - variable:
+ name: ObsType/stationPressure
+ is_in: 183
+
+
+ # GeoVaLs for Driving Observation Operators (testing mode)
+ # --------------------------------------------------------
+ geovals:
+ filename: "{{atmosphere_obsdatain_path}}/{{atmosphere_obsdatain_prefix}}{{observation_from_jcb}}_geoval{{atmosphere_obsdatain_suffix}}"
+
+ # Passed benchmark for UFO testing
+ # --------------------------------
+ passedBenchmark: 0
diff --git a/parm/jcb-gdas/observations/atmosphere/sondes.yaml.j2 b/parm/jcb-gdas/observations/atmosphere/sondes.yaml.j2
new file mode 100644
index 000000000..62cc621b8
--- /dev/null
+++ b/parm/jcb-gdas/observations/atmosphere/sondes.yaml.j2
@@ -0,0 +1,131 @@
+-
+
+ # Observation Space (I/O)
+ # -----------------------
+ obs space:
+ name: {{observation_from_jcb}}
+ obsdatain:
+ engine:
+ type: H5File
+ obsfile: "{{atmosphere_obsdatain_path}}/{{atmosphere_obsdatain_prefix}}{{observation_from_jcb}}{{atmosphere_obsdatain_suffix}}"
+ missing file action: warn
+ obsgrouping:
+ group variables: ["stationIdentification"]
+ sort variable: "pressure"
+ sort order: "descending"
+ obsdataout:
+ engine:
+ type: H5File
+ obsfile: "{{atmosphere_obsdataout_path}}/{{atmosphere_obsdataout_prefix}}{{observation_from_jcb}}{{atmosphere_obsdataout_suffix}}"
+ io pool:
+ max pool size: 1
+ simulated variables: [stationPressure, airTemperature, virtualTemperature, windEastward, windNorthward,
+ specificHumidity]
+
+ # Observation Operator
+ # --------------------
+ obs operator:
+ name: Composite
+ components:
+ - name: VertInterp
+ variables:
+ - name: airTemperature
+ - name: virtualTemperature
+ - name: windEastward
+ - name: windNorthward
+ - name: specificHumidity
+ - name: SfcCorrected
+ correction scheme to use: GSL
+ geovar_sfc_geomz: geopotential_height_at_surface
+ geovar_geomz: geopotential_height
+ variables:
+ - name: stationPressure
+
+ # Linear Observation Operator
+ # ---------------------------
+ linear obs operator:
+ name: Composite
+ components:
+ - name: VertInterp
+ variables:
+ - name: airTemperature
+ - name: virtualTemperature
+ - name: windEastward
+ - name: windNorthward
+ - name: specificHumidity
+ - name: Identity
+ variables:
+ - name: stationPressure
+
+ # Observation Filters (QC)
+ # ------------------------
+ obs filters:
+ #
+ # Reject all obs with PreQC mark already set above 3
+ - filter: PreQC
+ maxvalue: 3.0
+ action:
+ name: reject
+ #
+ # Observation Range Sanity Check
+ - filter: Bounds Check
+ filter variables:
+ - name: stationPressure
+ minvalue: 37499.0
+ maxvalue: 106999.0
+ action:
+ name: reject
+ #
+ # Assign obsError
+ - filter: Perform Action
+ filter variables:
+ - name: stationPressure
+ action:
+ name: assign error
+ error parameter: 100.0 # 1.0 hPa
+ #
+ # Assign the initial observation error, based on height/pressure
+ - filter: Perform Action
+ filter variables:
+ - name: stationPressure
+ action:
+ name: assign error
+ error function:
+ name: ObsErrorModelStepwiseLinear@ObsFunction
+ options:
+ xvar:
+ name: ObsValue/stationPressure
+ xvals: [80000.0, 75000.0]
+ errors: [110.0, 120.0] # 1.1 mb below 800 mb and 1.2 mb agove 750 mb
+ #
+ - filter: Perform Action
+ filter variables:
+ - name: stationPressure
+ action:
+ name: inflate error
+ inflation variable:
+ name: ObsErrorFactorSfcPressure@ObsFunction
+ options:
+ error_min: 100.0 # 1 mb
+ error_max: 300.0 # 3 mb
+ geovar_geomz: geopotential_height
+ geovar_sfc_geomz: geopotential_height_at_surface
+ #
+ # Gross error check with (O - B) / ObsError greater than threshold
+ - filter: Background Check
+ filter variables:
+ - name: stationPressure
+ threshold: 3.6
+ absolute threshold: 990.0
+ action:
+ name: reject
+
+
+ # GeoVaLs for Driving Observation Operators (testing mode)
+ # --------------------------------------------------------
+ geovals:
+ filename: "{{atmosphere_obsdatain_path}}/{{atmosphere_obsdatain_prefix}}{{observation_from_jcb}}_geoval{{atmosphere_obsdatain_suffix}}"
+
+ # Passed benchmark for UFO testing
+ # --------------------------------
+ passedBenchmark: 0
diff --git a/parm/jcb-gdas/observations/marine/adt_rads_all.yaml.j2 b/parm/jcb-gdas/observations/marine/adt_rads_all.yaml.j2
new file mode 100644
index 000000000..a82f710d2
--- /dev/null
+++ b/parm/jcb-gdas/observations/marine/adt_rads_all.yaml.j2
@@ -0,0 +1,78 @@
+- obs space:
+ name: {{observation_from_jcb}}
+ obsdatain:
+ engine:
+ type: H5File
+ obsfile: "{{marine_obsdatain_path}}/{{marine_obsdatain_prefix}}{{observation_from_jcb}}{{marine_obsdatain_suffix}}"
+ missing file action: warn
+ obsdataout:
+ engine:
+ type: H5File
+ obsfile: "{{marine_obsdataout_path}}/{{marine_obsdataout_prefix}}{{observation_from_jcb}}{{marine_obsdataout_suffix}}"
+ simulated variables: [absoluteDynamicTopography]
+ io pool:
+ max pool size: 1
+{% if marine_letkf_app | default(false) %}
+ distribution:
+ name: Halo
+ halo size: {{ marine_letkf_dist_halo_size }}
+{% endif %}
+ get values:
+ time interpolation: linear
+ obs operator:
+ name: ADT
+ obs error:
+ covariance model: diagonal
+ obs filters:
+ - filter: Domain Check
+ where:
+ - variable: {name: GeoVaLs/sea_area_fraction}
+ value: is_valid
+ minvalue: 0.9
+ - filter: Domain Check
+ where:
+ - variable: { name: GeoVaLs/sea_surface_temperature}
+ minvalue: 5.0
+ - filter: Background Check
+ absolute threshold: 1.0
+ - filter: Domain Check
+ where:
+ - variable: {name: GeoVaLs/sea_floor_depth_below_sea_surface}
+ minvalue: 500
+ - filter: Perform Action
+ action:
+ name: assign error
+ error function:
+ name: ObsFunction/LinearCombination
+ options:
+ variables: [GeoVaLs/mesoscale_representation_error,
+ ObsError/absoluteDynamicTopography]
+ coefs: [0.2,
+ 3.0]
+ - filter: Domain Check
+ where:
+ - variable: { name: GeoVaLs/sea_ice_area_fraction}
+ maxvalue: 0.00001
+ - filter: Domain Check
+ where:
+ - variable: {name: GeoVaLs/distance_from_coast}
+ minvalue: 50e3
+ - filter: BlackList
+ where:
+ - variable:
+ name: MetaData/latitude
+ minvalue: 4
+ maxvalue: 30
+ - variable:
+ name: MetaData/longitude
+ minvalue: 32
+ maxvalue: 56
+{% if marine_letkf_app | default(false) %}
+ obs localizations:
+ - localization method: Rossby
+ base value: 100.0e3
+ rossby mult: 1.0
+ min grid mult: 2.0
+ min value: 200.0e3
+ max value: 900.0e3
+{% endif %}
diff --git a/parm/jcb-gdas/observations/marine/adt_rads_cryosat2.yaml.j2 b/parm/jcb-gdas/observations/marine/adt_rads_cryosat2.yaml.j2
new file mode 120000
index 000000000..02ad0a9d7
--- /dev/null
+++ b/parm/jcb-gdas/observations/marine/adt_rads_cryosat2.yaml.j2
@@ -0,0 +1 @@
+adt_rads_all.yaml.j2
\ No newline at end of file
diff --git a/parm/jcb-gdas/observations/marine/adt_rads_jason3.yaml.j2 b/parm/jcb-gdas/observations/marine/adt_rads_jason3.yaml.j2
new file mode 120000
index 000000000..02ad0a9d7
--- /dev/null
+++ b/parm/jcb-gdas/observations/marine/adt_rads_jason3.yaml.j2
@@ -0,0 +1 @@
+adt_rads_all.yaml.j2
\ No newline at end of file
diff --git a/parm/jcb-gdas/observations/marine/adt_rads_saral.yaml.j2 b/parm/jcb-gdas/observations/marine/adt_rads_saral.yaml.j2
new file mode 120000
index 000000000..02ad0a9d7
--- /dev/null
+++ b/parm/jcb-gdas/observations/marine/adt_rads_saral.yaml.j2
@@ -0,0 +1 @@
+adt_rads_all.yaml.j2
\ No newline at end of file
diff --git a/parm/jcb-gdas/observations/marine/adt_rads_sentinel3a.yaml.j2 b/parm/jcb-gdas/observations/marine/adt_rads_sentinel3a.yaml.j2
new file mode 120000
index 000000000..02ad0a9d7
--- /dev/null
+++ b/parm/jcb-gdas/observations/marine/adt_rads_sentinel3a.yaml.j2
@@ -0,0 +1 @@
+adt_rads_all.yaml.j2
\ No newline at end of file
diff --git a/parm/jcb-gdas/observations/marine/adt_rads_sentinel3b.yaml.j2 b/parm/jcb-gdas/observations/marine/adt_rads_sentinel3b.yaml.j2
new file mode 120000
index 000000000..02ad0a9d7
--- /dev/null
+++ b/parm/jcb-gdas/observations/marine/adt_rads_sentinel3b.yaml.j2
@@ -0,0 +1 @@
+adt_rads_all.yaml.j2
\ No newline at end of file
diff --git a/parm/jcb-gdas/observations/marine/adt_rads_sentinel6a.yaml.j2 b/parm/jcb-gdas/observations/marine/adt_rads_sentinel6a.yaml.j2
new file mode 120000
index 000000000..02ad0a9d7
--- /dev/null
+++ b/parm/jcb-gdas/observations/marine/adt_rads_sentinel6a.yaml.j2
@@ -0,0 +1 @@
+adt_rads_all.yaml.j2
\ No newline at end of file
diff --git a/parm/jcb-gdas/observations/marine/adt_rads_swot.yaml.j2 b/parm/jcb-gdas/observations/marine/adt_rads_swot.yaml.j2
new file mode 120000
index 000000000..02ad0a9d7
--- /dev/null
+++ b/parm/jcb-gdas/observations/marine/adt_rads_swot.yaml.j2
@@ -0,0 +1 @@
+adt_rads_all.yaml.j2
\ No newline at end of file
diff --git a/parm/jcb-gdas/observations/marine/icec_abi_g16_l2.yaml.j2 b/parm/jcb-gdas/observations/marine/icec_abi_g16_l2.yaml.j2
new file mode 120000
index 000000000..3ebe0973c
--- /dev/null
+++ b/parm/jcb-gdas/observations/marine/icec_abi_g16_l2.yaml.j2
@@ -0,0 +1 @@
+icec_generic_passive.yaml.j2
\ No newline at end of file
diff --git a/parm/jcb-gdas/observations/marine/icec_amsr2_north.yaml.j2 b/parm/jcb-gdas/observations/marine/icec_amsr2_north.yaml.j2
new file mode 100644
index 000000000..5696bdc66
--- /dev/null
+++ b/parm/jcb-gdas/observations/marine/icec_amsr2_north.yaml.j2
@@ -0,0 +1,65 @@
+- obs space:
+ name: {{observation_from_jcb}}
+ obsdatain:
+ engine:
+ type: H5File
+ obsfile: "{{marine_obsdatain_path}}/{{marine_obsdatain_prefix}}{{observation_from_jcb}}{{marine_obsdatain_suffix}}"
+ missing file action: warn
+ obsdataout:
+ engine:
+ type: H5File
+ obsfile: "{{marine_obsdataout_path}}/{{marine_obsdataout_prefix}}{{observation_from_jcb}}{{marine_obsdataout_suffix}}"
+ simulated variables: [seaIceFraction]
+ io pool:
+ max pool size: 1
+{% if marine_letkf_app | default(false) %}
+ distribution:
+ name: Halo
+ halo size: {{ marine_letkf_dist_halo_size }}
+{% endif %}
+ get values:
+ time interpolation: linear
+ obs operator:
+ name: Identity
+ observation alias file: obsop_name_map.yaml
+ obs error:
+ covariance model: diagonal
+ obs filters:
+ - filter: Domain Check
+ where:
+ - variable: {name: GeoVaLs/sea_area_fraction}
+ value: is_valid
+ minvalue: 0.9
+ - filter: Bounds Check
+ minvalue: 0.0
+ maxvalue: 1.0
+ - filter: Background Check
+ absolute threshold: 0.5
+ - filter: Domain Check
+ where:
+ - variable: { name: GeoVaLs/sea_surface_temperature}
+ maxvalue: 2.0
+ - filter: Domain Check
+ where:
+ - variable: { name: GeoVaLs/sea_surface_temperature}
+ maxvalue: 0.0
+ action:
+ name: inflate error
+ inflation factor: 2.0
+{% if marine_letkf_app | default(false) %}
+ - filter: Gaussian Thinning
+ horizontal_mesh: 25 #km
+ use_reduced_horizontal_grid: true
+ select_median: true
+ action:
+ name: reduce obs space
+{% endif %}
+{% if marine_letkf_app | default(false) %}
+ obs localizations:
+ - localization method: Rossby
+ base value: 100.0e3
+ rossby mult: 1.0
+ min grid mult: 2.0
+ min value: 200.0e3
+ max value: 900.0e3
+{% endif %}
diff --git a/parm/jcb-gdas/observations/marine/icec_amsr2_south.yaml.j2 b/parm/jcb-gdas/observations/marine/icec_amsr2_south.yaml.j2
new file mode 100644
index 000000000..5696bdc66
--- /dev/null
+++ b/parm/jcb-gdas/observations/marine/icec_amsr2_south.yaml.j2
@@ -0,0 +1,65 @@
+- obs space:
+ name: {{observation_from_jcb}}
+ obsdatain:
+ engine:
+ type: H5File
+ obsfile: "{{marine_obsdatain_path}}/{{marine_obsdatain_prefix}}{{observation_from_jcb}}{{marine_obsdatain_suffix}}"
+ missing file action: warn
+ obsdataout:
+ engine:
+ type: H5File
+ obsfile: "{{marine_obsdataout_path}}/{{marine_obsdataout_prefix}}{{observation_from_jcb}}{{marine_obsdataout_suffix}}"
+ simulated variables: [seaIceFraction]
+ io pool:
+ max pool size: 1
+{% if marine_letkf_app | default(false) %}
+ distribution:
+ name: Halo
+ halo size: {{ marine_letkf_dist_halo_size }}
+{% endif %}
+ get values:
+ time interpolation: linear
+ obs operator:
+ name: Identity
+ observation alias file: obsop_name_map.yaml
+ obs error:
+ covariance model: diagonal
+ obs filters:
+ - filter: Domain Check
+ where:
+ - variable: {name: GeoVaLs/sea_area_fraction}
+ value: is_valid
+ minvalue: 0.9
+ - filter: Bounds Check
+ minvalue: 0.0
+ maxvalue: 1.0
+ - filter: Background Check
+ absolute threshold: 0.5
+ - filter: Domain Check
+ where:
+ - variable: { name: GeoVaLs/sea_surface_temperature}
+ maxvalue: 2.0
+ - filter: Domain Check
+ where:
+ - variable: { name: GeoVaLs/sea_surface_temperature}
+ maxvalue: 0.0
+ action:
+ name: inflate error
+ inflation factor: 2.0
+{% if marine_letkf_app | default(false) %}
+ - filter: Gaussian Thinning
+ horizontal_mesh: 25 #km
+ use_reduced_horizontal_grid: true
+ select_median: true
+ action:
+ name: reduce obs space
+{% endif %}
+{% if marine_letkf_app | default(false) %}
+ obs localizations:
+ - localization method: Rossby
+ base value: 100.0e3
+ rossby mult: 1.0
+ min grid mult: 2.0
+ min value: 200.0e3
+ max value: 900.0e3
+{% endif %}
diff --git a/parm/jcb-gdas/observations/marine/icec_amsu_ma1_l2.yaml.j2 b/parm/jcb-gdas/observations/marine/icec_amsu_ma1_l2.yaml.j2
new file mode 120000
index 000000000..3ebe0973c
--- /dev/null
+++ b/parm/jcb-gdas/observations/marine/icec_amsu_ma1_l2.yaml.j2
@@ -0,0 +1 @@
+icec_generic_passive.yaml.j2
\ No newline at end of file
diff --git a/parm/jcb-gdas/observations/marine/icec_amsu_mb_l2.yaml.j2 b/parm/jcb-gdas/observations/marine/icec_amsu_mb_l2.yaml.j2
new file mode 120000
index 000000000..3ebe0973c
--- /dev/null
+++ b/parm/jcb-gdas/observations/marine/icec_amsu_mb_l2.yaml.j2
@@ -0,0 +1 @@
+icec_generic_passive.yaml.j2
\ No newline at end of file
diff --git a/parm/jcb-gdas/observations/marine/icec_atms_n20_l2.yaml.j2 b/parm/jcb-gdas/observations/marine/icec_atms_n20_l2.yaml.j2
new file mode 120000
index 000000000..3ebe0973c
--- /dev/null
+++ b/parm/jcb-gdas/observations/marine/icec_atms_n20_l2.yaml.j2
@@ -0,0 +1 @@
+icec_generic_passive.yaml.j2
\ No newline at end of file
diff --git a/parm/jcb-gdas/observations/marine/icec_atms_n21_l2.yaml.j2 b/parm/jcb-gdas/observations/marine/icec_atms_n21_l2.yaml.j2
new file mode 120000
index 000000000..3ebe0973c
--- /dev/null
+++ b/parm/jcb-gdas/observations/marine/icec_atms_n21_l2.yaml.j2
@@ -0,0 +1 @@
+icec_generic_passive.yaml.j2
\ No newline at end of file
diff --git a/parm/jcb-gdas/observations/marine/icec_atms_npp_l2.yaml.j2 b/parm/jcb-gdas/observations/marine/icec_atms_npp_l2.yaml.j2
new file mode 120000
index 000000000..3ebe0973c
--- /dev/null
+++ b/parm/jcb-gdas/observations/marine/icec_atms_npp_l2.yaml.j2
@@ -0,0 +1 @@
+icec_generic_passive.yaml.j2
\ No newline at end of file
diff --git a/parm/jcb-gdas/observations/marine/icec_generic_passive.yaml.j2 b/parm/jcb-gdas/observations/marine/icec_generic_passive.yaml.j2
new file mode 100644
index 000000000..8526710ae
--- /dev/null
+++ b/parm/jcb-gdas/observations/marine/icec_generic_passive.yaml.j2
@@ -0,0 +1,73 @@
+- obs space:
+ name: {{observation_from_jcb}}
+ obsdatain:
+ engine:
+ type: H5File
+ obsfile: "{{marine_obsdatain_path}}/{{marine_obsdatain_prefix}}{{observation_from_jcb}}{{marine_obsdatain_suffix}}"
+ missing file action: warn
+ obsdataout:
+ engine:
+ type: H5File
+ obsfile: "{{marine_obsdataout_path}}/{{marine_obsdataout_prefix}}{{observation_from_jcb}}{{marine_obsdataout_suffix}}"
+ simulated variables: [seaIceFraction]
+ io pool:
+ max pool size: 1
+{% if marine_letkf_app | default(false) %}
+ distribution:
+ name: Halo
+ halo size: {{ marine_letkf_dist_halo_size }}
+{% endif %}
+ get values:
+ time interpolation: linear
+ obs operator:
+ name: Identity
+ observation alias file: obsop_name_map.yaml
+ obs error:
+ covariance model: diagonal
+ obs filters:
+ - filter: Domain Check
+ where:
+ - variable: {name: GeoVaLs/sea_area_fraction}
+ value: is_valid
+ minvalue: 0.9
+ - filter: Bounds Check
+ minvalue: 0.0
+ maxvalue: 1.0
+ #- filter: Background Check
+ # threshold: 5.0
+ - filter: Domain Check
+ where:
+ - variable: { name: GeoVaLs/sea_surface_temperature}
+ maxvalue: 2.0
+ - filter: Domain Check
+ where:
+ - variable: { name: GeoVaLs/sea_surface_temperature}
+ maxvalue: 0.0
+ action:
+ name: inflate error
+ inflation factor: 2.0
+ - filter: Domain Check
+ where:
+ - variable: {name: GeoVaLs/distance_from_coast}
+ minvalue: 0e3
+ - filter: Gaussian Thinning
+ horizontal_mesh: 25 #km
+ use_reduced_horizontal_grid: true
+ select_median: true
+ action:
+ name: reduce obs space
+ - filter: Domain Check
+ action:
+ name: passivate
+ where:
+ - variable: {name: GeoVaLs/sea_surface_temperature}
+ maxvalue: -4.0
+{% if marine_letkf_app | default(false) %}
+ obs localizations:
+ - localization method: Rossby
+ base value: 100.0e3
+ rossby mult: 1.0
+ min grid mult: 2.0
+ min value: 200.0e3
+ max value: 900.0e3
+{% endif %}
diff --git a/parm/jcb-gdas/observations/marine/icec_gmi_gpm_l2.yaml.j2 b/parm/jcb-gdas/observations/marine/icec_gmi_gpm_l2.yaml.j2
new file mode 120000
index 000000000..3ebe0973c
--- /dev/null
+++ b/parm/jcb-gdas/observations/marine/icec_gmi_gpm_l2.yaml.j2
@@ -0,0 +1 @@
+icec_generic_passive.yaml.j2
\ No newline at end of file
diff --git a/parm/jcb-gdas/observations/marine/icec_ssmis_f17_l2.yaml.j2 b/parm/jcb-gdas/observations/marine/icec_ssmis_f17_l2.yaml.j2
new file mode 100644
index 000000000..ac83a5e80
--- /dev/null
+++ b/parm/jcb-gdas/observations/marine/icec_ssmis_f17_l2.yaml.j2
@@ -0,0 +1,73 @@
+- obs space:
+ name: {{observation_from_jcb}}
+ obsdatain:
+ engine:
+ type: H5File
+ obsfile: "{{marine_obsdatain_path}}/{{marine_obsdatain_prefix}}{{observation_from_jcb}}{{marine_obsdatain_suffix}}"
+ missing file action: warn
+ obsdataout:
+ engine:
+ type: H5File
+ obsfile: "{{marine_obsdataout_path}}/{{marine_obsdataout_prefix}}{{observation_from_jcb}}{{marine_obsdataout_suffix}}"
+ simulated variables: [seaIceFraction]
+ io pool:
+ max pool size: 1
+{% if marine_letkf_app | default(false) %}
+ distribution:
+ name: Halo
+ halo size: {{ marine_letkf_dist_halo_size }}
+{% endif %}
+ get values:
+ time interpolation: linear
+ obs operator:
+ name: Identity
+ observation alias file: obsop_name_map.yaml
+ obs error:
+ covariance model: diagonal
+ obs filters:
+ - filter: Domain Check
+ where:
+ - variable: {name: GeoVaLs/sea_area_fraction}
+ value: is_valid
+ minvalue: 0.9
+ - filter: Bounds Check
+ minvalue: 0.0
+ maxvalue: 1.0
+ #- filter: Background Check
+ # threshold: 5.0
+ - filter: Domain Check
+ where:
+ - variable: { name: GeoVaLs/sea_surface_temperature}
+ maxvalue: 2.0
+ - filter: Domain Check
+ where:
+ - variable: { name: GeoVaLs/sea_surface_temperature}
+ maxvalue: 0.0
+ action:
+ name: inflate error
+ inflation factor: 2.0
+ - filter: Domain Check
+ where:
+ - variable: {name: GeoVaLs/distance_from_coast}
+ minvalue: 0e3
+ - filter: Gaussian Thinning
+ horizontal_mesh: 25 #km
+ use_reduced_horizontal_grid: true
+ select_median: true
+ action:
+ name: reduce obs space
+# - filter: Domain Check
+# action:
+# name: passivate
+# where:
+# - variable: {name: GeoVaLs/sea_surface_temperature}
+# maxvalue: -4.0
+{% if marine_letkf_app | default(false) %}
+ obs localizations:
+ - localization method: Rossby
+ base value: 100.0e3
+ rossby mult: 1.0
+ min grid mult: 2.0
+ min value: 200.0e3
+ max value: 900.0e3
+{% endif %}
diff --git a/parm/jcb-gdas/observations/marine/icec_viirs_j01_l2.yaml.j2 b/parm/jcb-gdas/observations/marine/icec_viirs_j01_l2.yaml.j2
new file mode 120000
index 000000000..3ebe0973c
--- /dev/null
+++ b/parm/jcb-gdas/observations/marine/icec_viirs_j01_l2.yaml.j2
@@ -0,0 +1 @@
+icec_generic_passive.yaml.j2
\ No newline at end of file
diff --git a/parm/jcb-gdas/observations/marine/icec_viirs_n20_l2_north.yaml.j2 b/parm/jcb-gdas/observations/marine/icec_viirs_n20_l2_north.yaml.j2
new file mode 120000
index 000000000..3ebe0973c
--- /dev/null
+++ b/parm/jcb-gdas/observations/marine/icec_viirs_n20_l2_north.yaml.j2
@@ -0,0 +1 @@
+icec_generic_passive.yaml.j2
\ No newline at end of file
diff --git a/parm/jcb-gdas/observations/marine/icec_viirs_n20_l2_south.yaml.j2 b/parm/jcb-gdas/observations/marine/icec_viirs_n20_l2_south.yaml.j2
new file mode 120000
index 000000000..3ebe0973c
--- /dev/null
+++ b/parm/jcb-gdas/observations/marine/icec_viirs_n20_l2_south.yaml.j2
@@ -0,0 +1 @@
+icec_generic_passive.yaml.j2
\ No newline at end of file
diff --git a/parm/jcb-gdas/observations/marine/icec_viirs_n21_l2.yaml.j2 b/parm/jcb-gdas/observations/marine/icec_viirs_n21_l2.yaml.j2
new file mode 120000
index 000000000..3ebe0973c
--- /dev/null
+++ b/parm/jcb-gdas/observations/marine/icec_viirs_n21_l2.yaml.j2
@@ -0,0 +1 @@
+icec_generic_passive.yaml.j2
\ No newline at end of file
diff --git a/parm/jcb-gdas/observations/marine/icec_viirs_npp_l2.yaml.j2 b/parm/jcb-gdas/observations/marine/icec_viirs_npp_l2.yaml.j2
new file mode 120000
index 000000000..3ebe0973c
--- /dev/null
+++ b/parm/jcb-gdas/observations/marine/icec_viirs_npp_l2.yaml.j2
@@ -0,0 +1 @@
+icec_generic_passive.yaml.j2
\ No newline at end of file
diff --git a/parm/jcb-gdas/observations/marine/insitu_profile_bathy.yaml.j2 b/parm/jcb-gdas/observations/marine/insitu_profile_bathy.yaml.j2
new file mode 100644
index 000000000..fe8bea759
--- /dev/null
+++ b/parm/jcb-gdas/observations/marine/insitu_profile_bathy.yaml.j2
@@ -0,0 +1,44 @@
+- obs space:
+ name: {{observation_from_jcb}}
+ obsdatain:
+ engine:
+ type: H5File
+ obsfile: "{{marine_obsdatain_path}}/{{marine_obsdatain_prefix}}{{observation_from_jcb}}{{marine_obsdatain_suffix}}"
+ missing file action: warn
+ obsdataout:
+ engine:
+ type: H5File
+ obsfile: "{{marine_obsdataout_path}}/{{marine_obsdataout_prefix}}{{observation_from_jcb}}{{marine_obsdataout_suffix}}"
+ simulated variables: [waterTemperature]
+ observed variables: [waterTemperature]
+ io pool:
+ max pool size: 1
+{% if marine_letkf_app | default(false) %}
+ distribution:
+ name: Halo
+ halo size: {{ marine_letkf_dist_halo_size }}
+{% endif %}
+ obs operator:
+ name: InsituTemperature
+ obs error:
+ covariance model: diagonal
+ obs filters:
+ - filter: Perform Action
+ action:
+ name: assign error
+ error function:
+ name: ObsFunction/LinearCombination
+ options:
+ variables:
+ - ObsError/waterTemperature
+ coefs:
+ - 1000.0
+{% if marine_letkf_app | default(false) %}
+ obs localizations:
+ - localization method: Rossby
+ base value: 100.0e3
+ rossby mult: 1.0
+ min grid mult: 2.0
+ min value: 200.0e3
+ max value: 900.0e3
+{% endif %}
diff --git a/parm/jcb-gdas/observations/marine/insitu_profile_glider.yaml.j2 b/parm/jcb-gdas/observations/marine/insitu_profile_glider.yaml.j2
new file mode 100644
index 000000000..513af6ccf
--- /dev/null
+++ b/parm/jcb-gdas/observations/marine/insitu_profile_glider.yaml.j2
@@ -0,0 +1,48 @@
+- obs space:
+ name: {{observation_from_jcb}}
+ obsdatain:
+ engine:
+ type: H5File
+ obsfile: "{{marine_obsdatain_path}}/{{marine_obsdatain_prefix}}{{observation_from_jcb}}{{marine_obsdatain_suffix}}"
+ missing file action: warn
+ obsdataout:
+ engine:
+ type: H5File
+ obsfile: "{{marine_obsdataout_path}}/{{marine_obsdataout_prefix}}{{observation_from_jcb}}{{marine_obsdataout_suffix}}"
+ simulated variables: [waterTemperature]
+ observed variables: [waterTemperature]
+ io pool:
+ max pool size: 1
+{% if marine_letkf_app | default(false) %}
+ distribution:
+ name: Halo
+ halo size: {{ marine_letkf_dist_halo_size }}
+{% endif %}
+ obs operator:
+ name: Composite
+ components:
+ - name: InsituTemperature
+ variables:
+ - name: waterTemperature
+ obs error:
+ covariance model: diagonal
+ obs filters:
+ - filter: Perform Action
+ action:
+ name: assign error
+ error function:
+ name: ObsFunction/LinearCombination
+ options:
+ variables:
+ - ObsError/waterTemperature
+ coefs:
+ - 1000.0
+{% if marine_letkf_app | default(false) %}
+ obs localizations:
+ - localization method: Rossby
+ base value: 100.0e3
+ rossby mult: 1.0
+ min grid mult: 2.0
+ min value: 200.0e3
+ max value: 900.0e3
+{% endif %}
diff --git a/parm/jcb-gdas/observations/marine/insitu_profile_marinemammal.yaml.j2 b/parm/jcb-gdas/observations/marine/insitu_profile_marinemammal.yaml.j2
new file mode 100644
index 000000000..513af6ccf
--- /dev/null
+++ b/parm/jcb-gdas/observations/marine/insitu_profile_marinemammal.yaml.j2
@@ -0,0 +1,48 @@
+- obs space:
+ name: {{observation_from_jcb}}
+ obsdatain:
+ engine:
+ type: H5File
+ obsfile: "{{marine_obsdatain_path}}/{{marine_obsdatain_prefix}}{{observation_from_jcb}}{{marine_obsdatain_suffix}}"
+ missing file action: warn
+ obsdataout:
+ engine:
+ type: H5File
+ obsfile: "{{marine_obsdataout_path}}/{{marine_obsdataout_prefix}}{{observation_from_jcb}}{{marine_obsdataout_suffix}}"
+ simulated variables: [waterTemperature]
+ observed variables: [waterTemperature]
+ io pool:
+ max pool size: 1
+{% if marine_letkf_app | default(false) %}
+ distribution:
+ name: Halo
+ halo size: {{ marine_letkf_dist_halo_size }}
+{% endif %}
+ obs operator:
+ name: Composite
+ components:
+ - name: InsituTemperature
+ variables:
+ - name: waterTemperature
+ obs error:
+ covariance model: diagonal
+ obs filters:
+ - filter: Perform Action
+ action:
+ name: assign error
+ error function:
+ name: ObsFunction/LinearCombination
+ options:
+ variables:
+ - ObsError/waterTemperature
+ coefs:
+ - 1000.0
+{% if marine_letkf_app | default(false) %}
+ obs localizations:
+ - localization method: Rossby
+ base value: 100.0e3
+ rossby mult: 1.0
+ min grid mult: 2.0
+ min value: 200.0e3
+ max value: 900.0e3
+{% endif %}
diff --git a/parm/jcb-gdas/observations/marine/insitu_profile_tesac.yaml.j2 b/parm/jcb-gdas/observations/marine/insitu_profile_tesac.yaml.j2
new file mode 100644
index 000000000..9eb69b6b4
--- /dev/null
+++ b/parm/jcb-gdas/observations/marine/insitu_profile_tesac.yaml.j2
@@ -0,0 +1,46 @@
+- obs space:
+ name: {{observation_from_jcb}}
+ obsdatain:
+ engine:
+ type: H5File
+ obsfile: "{{marine_obsdatain_path}}/{{marine_obsdatain_prefix}}{{observation_from_jcb}}{{marine_obsdatain_suffix}}"
+ missing file action: warn
+ obsdataout:
+ engine:
+ type: H5File
+ obsfile: "{{marine_obsdataout_path}}/{{marine_obsdataout_prefix}}{{observation_from_jcb}}{{marine_obsdataout_suffix}}"
+ simulated variables: [waterTemperature]
+ observed variables: [waterTemperature]
+ io pool:
+ max pool size: 1
+{% if marine_letkf_app | default(false) %}
+ distribution:
+ name: Halo
+ halo size: {{ marine_letkf_dist_halo_size }}
+{% endif %}
+ obs operator:
+ name: Composite
+ components:
+ - name: InsituTemperature
+ variables:
+ - name: waterTemperature
+ obs filters:
+ - filter: Perform Action
+ action:
+ name: assign error
+ error function:
+ name: ObsFunction/LinearCombination
+ options:
+ variables:
+ - ObsError/waterTemperature
+ coefs:
+ - 1000.0
+{% if marine_letkf_app | default(false) %}
+ obs localizations:
+ - localization method: Rossby
+ base value: 100.0e3
+ rossby mult: 1.0
+ min grid mult: 2.0
+ min value: 200.0e3
+ max value: 900.0e3
+{% endif %}
diff --git a/parm/jcb-gdas/observations/marine/insitu_profile_tesac_salinity.yaml.j2 b/parm/jcb-gdas/observations/marine/insitu_profile_tesac_salinity.yaml.j2
new file mode 100644
index 000000000..6a0fe7553
--- /dev/null
+++ b/parm/jcb-gdas/observations/marine/insitu_profile_tesac_salinity.yaml.j2
@@ -0,0 +1,48 @@
+- obs space:
+ name: {{observation_from_jcb}}
+ obsdatain:
+ engine:
+ type: H5File
+ obsfile: "{{marine_obsdatain_path}}/{{marine_obsdatain_prefix}}{{observation_from_jcb}}{{marine_obsdatain_suffix}}"
+ missing file action: warn
+ obsdataout:
+ engine:
+ type: H5File
+ obsfile: "{{marine_obsdataout_path}}/{{marine_obsdataout_prefix}}{{observation_from_jcb}}{{marine_obsdataout_suffix}}"
+ simulated variables: [salinity]
+ observed variables: [salinity]
+ io pool:
+ max pool size: 1
+{% if marine_letkf_app | default(false) %}
+ distribution:
+ name: Halo
+ halo size: {{ marine_letkf_dist_halo_size }}
+{% endif %}
+ obs operator:
+ name: VertInterp
+ observation alias file: ./obsop_name_map.yaml
+ vertical coordinate: sea_water_depth
+ observation vertical coordinate: depth
+ interpolation method: linear
+ obs error:
+ covariance model: diagonal
+ obs filters:
+ - filter: Perform Action
+ action:
+ name: assign error
+ error function:
+ name: ObsFunction/LinearCombination
+ options:
+ variables:
+ - ObsError/salinity
+ coefs:
+ - 1000.0
+{% if marine_letkf_app | default(false) %}
+ obs localizations:
+ - localization method: Rossby
+ base value: 100.0e3
+ rossby mult: 1.0
+ min grid mult: 2.0
+ min value: 200.0e3
+ max value: 900.0e3
+{% endif %}
diff --git a/parm/jcb-gdas/observations/marine/insitu_profile_tropical.yaml.j2 b/parm/jcb-gdas/observations/marine/insitu_profile_tropical.yaml.j2
new file mode 100644
index 000000000..83c5788b2
--- /dev/null
+++ b/parm/jcb-gdas/observations/marine/insitu_profile_tropical.yaml.j2
@@ -0,0 +1,54 @@
+- obs space:
+ name: {{observation_from_jcb}}
+ obsdatain:
+ engine:
+ type: H5File
+ obsfile: "{{marine_obsdatain_path}}/{{marine_obsdatain_prefix}}{{observation_from_jcb}}{{marine_obsdatain_suffix}}"
+ missing file action: warn
+ obsdataout:
+ engine:
+ type: H5File
+ obsfile: "{{marine_obsdataout_path}}/{{marine_obsdataout_prefix}}{{observation_from_jcb}}{{marine_obsdataout_suffix}}"
+ simulated variables: [waterTemperature]
+ observed variables: [waterTemperature]
+ io pool:
+ max pool size: 1
+{% if marine_letkf_app | default(false) %}
+ distribution:
+ name: Halo
+ halo size: {{ marine_letkf_dist_halo_size }}
+{% endif %}
+ obs operator:
+ name: Composite
+ components:
+ - name: InsituTemperature
+ variables:
+ - name: waterTemperature
+ obs error:
+ covariance model: diagonal
+ obs filters:
+ - filter: Perform Action
+ action:
+ name: assign error
+ error function:
+ name: ObsFunction/LinearCombination
+ options:
+ variables:
+ - ObsError/waterTemperature
+ coefs:
+ - 100.0
+ - filter: Domain Check
+ action:
+ name: passivate
+ where:
+ - variable: {name: GeoVaLs/sea_surface_temperature}
+ maxvalue: -4.0
+{% if marine_letkf_app | default(false) %}
+ obs localizations:
+ - localization method: Rossby
+ base value: 100.0e3
+ rossby mult: 1.0
+ min grid mult: 2.0
+ min value: 200.0e3
+ max value: 900.0e3
+{% endif %}
diff --git a/parm/jcb-gdas/observations/marine/insitu_profile_xbtctd.yaml.j2 b/parm/jcb-gdas/observations/marine/insitu_profile_xbtctd.yaml.j2
new file mode 100644
index 000000000..513af6ccf
--- /dev/null
+++ b/parm/jcb-gdas/observations/marine/insitu_profile_xbtctd.yaml.j2
@@ -0,0 +1,48 @@
+- obs space:
+ name: {{observation_from_jcb}}
+ obsdatain:
+ engine:
+ type: H5File
+ obsfile: "{{marine_obsdatain_path}}/{{marine_obsdatain_prefix}}{{observation_from_jcb}}{{marine_obsdatain_suffix}}"
+ missing file action: warn
+ obsdataout:
+ engine:
+ type: H5File
+ obsfile: "{{marine_obsdataout_path}}/{{marine_obsdataout_prefix}}{{observation_from_jcb}}{{marine_obsdataout_suffix}}"
+ simulated variables: [waterTemperature]
+ observed variables: [waterTemperature]
+ io pool:
+ max pool size: 1
+{% if marine_letkf_app | default(false) %}
+ distribution:
+ name: Halo
+ halo size: {{ marine_letkf_dist_halo_size }}
+{% endif %}
+ obs operator:
+ name: Composite
+ components:
+ - name: InsituTemperature
+ variables:
+ - name: waterTemperature
+ obs error:
+ covariance model: diagonal
+ obs filters:
+ - filter: Perform Action
+ action:
+ name: assign error
+ error function:
+ name: ObsFunction/LinearCombination
+ options:
+ variables:
+ - ObsError/waterTemperature
+ coefs:
+ - 1000.0
+{% if marine_letkf_app | default(false) %}
+ obs localizations:
+ - localization method: Rossby
+ base value: 100.0e3
+ rossby mult: 1.0
+ min grid mult: 2.0
+ min value: 200.0e3
+ max value: 900.0e3
+{% endif %}
diff --git a/parm/jcb-gdas/observations/marine/insitu_salt_profile_argo.yaml.j2 b/parm/jcb-gdas/observations/marine/insitu_salt_profile_argo.yaml.j2
new file mode 100644
index 000000000..c11b62483
--- /dev/null
+++ b/parm/jcb-gdas/observations/marine/insitu_salt_profile_argo.yaml.j2
@@ -0,0 +1,202 @@
+- obs space:
+ name: {{observation_from_jcb}}
+ obsdatain:
+ engine:
+ type: H5File
+ obsfile: "{{marine_obsdatain_path}}/{{marine_obsdatain_prefix}}{{observation_from_jcb}}{{marine_obsdatain_suffix}}"
+ missing file action: warn
+ obsgrouping:
+ group variables: [latitude, longitude, dateTime]
+ sort variable: depth
+ sort group: MetaData
+ sort order: ascending
+ obsdataout:
+ engine:
+ type: H5File
+ obsfile: "{{marine_obsdataout_path}}/{{marine_obsdataout_prefix}}{{observation_from_jcb}}{{marine_obsdataout_suffix}}"
+ simulated variables: [salinity]
+ observed variables: [salinity]
+ io pool:
+ max pool size: 1
+{% if marine_letkf_app | default(false) %}
+ distribution:
+ name: Halo
+ halo size: {{ marine_letkf_dist_halo_size }}
+{% endif %}
+ obs operator:
+ name: VertInterp
+ observation alias file: ./obsop_name_map.yaml
+ vertical coordinate: sea_water_depth
+ observation vertical coordinate: depth
+ interpolation method: linear
+ obs error:
+ covariance model: diagonal
+
+ #-------------------------------------------------------------------------------
+ # START OF OBS FILTERS (work done by Kriti Bhargava)
+ # The QC filters used here are based on the document by IODE that can be found at
+ # https://cdn.ioos.noaa.gov/media/2017/12/recommendations_in_situ_data_real_time_qc.pdf
+ #-------------------------------------------------------------------------------
+
+ obs filters:
+
+ # land check
+ - filter: Domain Check
+ where:
+ - variable: {name: GeoVaLs/sea_area_fraction}
+ value: is_valid
+ minvalue: 0.5
+
+
+ ## Filters for S:
+ #-------------------------------------------------------------------------------
+ #-----------------------------------------------------------------------------
+ ### Global range test
+ #-----------------------------------------------------------------------------
+
+ - filter: Bounds Check
+ filter variables: [{name: salinity}]
+ minvalue: 2.0
+ maxvalue: 41.0
+
+ #-----------------------------------------------------------------------------
+ ### Regional range test
+ #-----------------------------------------------------------------------------
+ #### Red Sea
+ #-----------------------------------------------------------------------------
+ ####
+ #### the document linked here describes Red sea as the are between 10N, 40E;
+ #### 20N, 50E; 30N, 30E; 10N, 40E. But that would also include Gulf of Aden.
+ #### A more reasonable choice seemed to be a box that extends from 10 N to
+ #### 30 N and 30 E to 45 East .
+
+ - filter: Bounds Check
+ filter variables: [{name: salinity}]
+ minvalue: 2.0
+ maxvalue: 41.0
+ where:
+ - variable:
+ name: MetaData/latitude
+ minvalue: 10
+ maxvalue: 30
+ - variable:
+ name: MetaData/longitude
+ minvalue: 30
+ maxvalue: 45
+
+ #### Mediterranean Sea
+ #-----------------------------------------------------------------------------
+ ##### Area 1/3 for Mediterranean Sea
+ - filter: Bounds Check
+ filter variables: [{name: salinity}]
+ minvalue: 2.0
+ maxvalue: 40.0
+ where:
+ - variable:
+ name: MetaData/latitude
+ minvalue: 30
+ maxvalue: 40
+ - variable:
+ name: MetaData/longitude
+ minvalue: -6
+ maxvalue: 40
+ ##### Area 2/3 for Mediterranean Sea
+ - filter: Bounds Check
+ filter variables: [{name: salinity}]
+ minvalue: 2.0
+ maxvalue: 40.0
+ where:
+ - variable:
+ name: MetaData/latitude
+ minvalue: 40
+ maxvalue: 41.5
+ - variable:
+ name: MetaData/longitude
+ minvalue: 20
+ maxvalue: 30
+ ##### Area 3/3 for Mediterranean Sea
+ - filter: Bounds Check
+ filter variables: [{name: salinity}]
+ minvalue: 2.0
+ maxvalue: 40.0
+ where:
+ - variable:
+ name: MetaData/latitude
+ minvalue: 40
+ maxvalue: 46
+ - variable:
+ name: MetaData/longitude
+ minvalue: 0
+ maxvalue: 20
+
+
+ #### Northwestern shelves
+ #-----------------------------------------------------------------------------
+
+ - filter: Bounds Check
+ filter variables: [{name: salinity}]
+ minvalue: 0.0
+ maxvalue: 37.0
+ where:
+ - variable:
+ name: MetaData/latitude
+ minvalue: 50
+ maxvalue: 60
+ - variable:
+ name: MetaData/longitude
+ minvalue: -20
+ maxvalue: 10
+
+ #### Southwestern shelves
+ #-----------------------------------------------------------------------------
+
+ - filter: Bounds Check
+ filter variables: [{name: salinity}]
+ minvalue: 0.0
+ maxvalue: 38
+ where:
+ - variable:
+ name: MetaData/latitude
+ minvalue: 25
+ maxvalue: 50
+ - variable:
+ name: MetaData/longitude
+ minvalue: -30
+ maxvalue: 0
+
+ #### Arctic Ocean
+ #-----------------------------------------------------------------------------
+
+ - filter: Bounds Check
+ filter variables: [{name: salinity}]
+ minvalue: 2.0
+ maxvalue: 40.0
+ where:
+ - variable:
+ name: MetaData/latitude
+ minvalue: 60
+
+ - filter: Background Check
+ filter variables: [{name: salinity}]
+ threshold: 5.0
+ absolute threshold: 5.0
+
+ - filter: Perform Action
+ action:
+ name: assign error
+ error function:
+ name: ObsFunction/LinearCombination
+ options:
+ variables:
+ - ObsError/salinity
+ coefs:
+ - 100.0
+{% if marine_letkf_app | default(false) %}
+ obs localizations:
+ - localization method: Rossby
+ base value: 100.0e3
+ rossby mult: 1.0
+ min grid mult: 2.0
+ min value: 200.0e3
+ max value: 900.0e3
+{% endif %}
diff --git a/parm/jcb-gdas/observations/marine/insitu_surface_altkob.yaml.j2 b/parm/jcb-gdas/observations/marine/insitu_surface_altkob.yaml.j2
new file mode 100644
index 000000000..aadad95f3
--- /dev/null
+++ b/parm/jcb-gdas/observations/marine/insitu_surface_altkob.yaml.j2
@@ -0,0 +1,45 @@
+- obs space:
+ name: {{observation_from_jcb}}
+ obsdatain:
+ engine:
+ type: H5File
+ obsfile: "{{marine_obsdatain_path}}/{{marine_obsdatain_prefix}}{{observation_from_jcb}}{{marine_obsdatain_suffix}}"
+ missing file action: warn
+ obsdataout:
+ engine:
+ type: H5File
+ obsfile: "{{marine_obsdataout_path}}/{{marine_obsdataout_prefix}}{{observation_from_jcb}}{{marine_obsdataout_suffix}}"
+ simulated variables: [seaSurfaceTemperature]
+ observed variables: [seaSurfaceTemperature]
+ io pool:
+ max pool size: 1
+{% if marine_letkf_app | default(false) %}
+ distribution:
+ name: Halo
+ halo size: {{ marine_letkf_dist_halo_size }}
+{% endif %}
+ obs operator:
+ name: Identity
+ observation alias file: obsop_name_map.yaml
+ obs error:
+ covariance model: diagonal
+ obs filters:
+ - filter: Perform Action
+ action:
+ name: assign error
+ error function:
+ name: ObsFunction/LinearCombination
+ options:
+ variables:
+ - ObsError/seaSurfaceTemperature
+ coefs:
+ - 1000.0
+{% if marine_letkf_app | default(false) %}
+ obs localizations:
+ - localization method: Rossby
+ base value: 100.0e3
+ rossby mult: 1.0
+ min grid mult: 2.0
+ min value: 200.0e3
+ max value: 900.0e3
+{% endif %}
diff --git a/parm/jcb-gdas/observations/marine/insitu_surface_dbuoyb_drifter.yaml.j2 b/parm/jcb-gdas/observations/marine/insitu_surface_dbuoyb_drifter.yaml.j2
new file mode 100644
index 000000000..b99ea1d04
--- /dev/null
+++ b/parm/jcb-gdas/observations/marine/insitu_surface_dbuoyb_drifter.yaml.j2
@@ -0,0 +1,61 @@
+- obs space:
+ name: {{observation_from_jcb}}
+ obsdatain:
+ engine:
+ type: H5File
+ obsfile: "{{marine_obsdatain_path}}/{{marine_obsdatain_prefix}}{{observation_from_jcb}}{{marine_obsdatain_suffix}}"
+ missing file action: warn
+ obsdataout:
+ engine:
+ type: H5File
+ obsfile: "{{marine_obsdataout_path}}/{{marine_obsdataout_prefix}}{{observation_from_jcb}}{{marine_obsdataout_suffix}}"
+ simulated variables: [seaSurfaceTemperature]
+ observed variables: [seaSurfaceTemperature]
+ io pool:
+ max pool size: 1
+{% if marine_letkf_app | default(false) %}
+ distribution:
+ name: Halo
+ halo size: {{ marine_letkf_dist_halo_size }}
+{% endif %}
+ get values:
+ time interpolation: linear
+ obs operator:
+ name: Identity
+ observation alias file: obsop_name_map.yaml
+ obs error:
+ covariance model: diagonal
+
+ obs pre filters:
+ - filter: Bounds Check
+ minvalue: -1.2
+ maxvalue: 41.0
+ - filter: Domain Check
+ where:
+ - variable: {name: ObsError/seaSurfaceTemperature}
+ minvalue: 1.0e-8
+
+ obs prior filters:
+ - filter: Domain Check
+ where:
+ - variable: {name: GeoVaLs/sea_area_fraction}
+ value: is_valid
+ minvalue: 0.9
+ - filter: Domain Check
+ where:
+ - variable: { name: GeoVaLs/sea_ice_area_fraction}
+ maxvalue: 1.0e-5
+ - filter: Domain Check
+ where:
+ - variable: {name: GeoVaLs/sea_surface_temperature}
+ minvalue: -1.2
+
+{% if marine_letkf_app | default(false) %}
+ obs localizations:
+ - localization method: Rossby
+ base value: 100.0e3
+ rossby mult: 1.0
+ min grid mult: 2.0
+ min value: 200.0e3
+ max value: 900.0e3
+{% endif %}
diff --git a/parm/jcb-gdas/observations/marine/insitu_surface_trkob.yaml.j2 b/parm/jcb-gdas/observations/marine/insitu_surface_trkob.yaml.j2
new file mode 100644
index 000000000..c4b8e8b51
--- /dev/null
+++ b/parm/jcb-gdas/observations/marine/insitu_surface_trkob.yaml.j2
@@ -0,0 +1,45 @@
+- obs space:
+ name: {{observation_from_jcb}}
+ obsdatain:
+ engine:
+ type: H5File
+ obsfile: "{{marine_obsdatain_path}}/{{marine_obsdatain_prefix}}{{observation_from_jcb}}{{marine_obsdatain_suffix}}"
+ missing file action: warn
+ obsdataout:
+ engine:
+ type: H5File
+ obsfile: "{{marine_obsdataout_path}}/{{marine_obsdataout_prefix}}{{observation_from_jcb}}{{marine_obsdataout_suffix}}"
+ simulated variables: [seaSurfaceTemperature]
+ observed variables: [seaSurfaceTemperature]
+ io pool:
+ max pool size: 1
+{% if marine_letkf_app | default(false) %}
+ distribution:
+ name: Halo
+ halo size: {{ marine_letkf_dist_halo_size }}
+{% endif %}
+ obs operator:
+ name: Identity
+ observation alias file: ./obsop_name_map.yaml
+ obs error:
+ covariance model: diagonal
+ obs filters:
+ - filter: Perform Action
+ action:
+ name: assign error
+ error function:
+ name: ObsFunction/LinearCombination
+ options:
+ variables:
+ - ObsError/seaSurfaceTemperature
+ coefs:
+ - 1000.0
+{% if marine_letkf_app | default(false) %}
+ obs localizations:
+ - localization method: Rossby
+ base value: 100.0e3
+ rossby mult: 1.0
+ min grid mult: 2.0
+ min value: 200.0e3
+ max value: 900.0e3
+{% endif %}
diff --git a/parm/jcb-gdas/observations/marine/insitu_surface_trkob_salinity.yaml.j2 b/parm/jcb-gdas/observations/marine/insitu_surface_trkob_salinity.yaml.j2
new file mode 100644
index 000000000..97f4c58f2
--- /dev/null
+++ b/parm/jcb-gdas/observations/marine/insitu_surface_trkob_salinity.yaml.j2
@@ -0,0 +1,45 @@
+- obs space:
+ name: {{observation_from_jcb}}
+ obsdatain:
+ engine:
+ type: H5File
+ obsfile: "{{marine_obsdatain_path}}/{{marine_obsdatain_prefix}}{{observation_from_jcb}}{{marine_obsdatain_suffix}}"
+ missing file action: warn
+ obsdataout:
+ engine:
+ type: H5File
+ obsfile: "{{marine_obsdataout_path}}/{{marine_obsdataout_prefix}}{{observation_from_jcb}}{{marine_obsdataout_suffix}}"
+ simulated variables: [seaSurfaceSalinity]
+ observed variables: [seaSurfaceSalinity]
+{% if marine_letkf_app | default(false) %}
+ distribution:
+ name: Halo
+ halo size: {{ marine_letkf_dist_halo_size }}
+{% endif %}
+ get values:
+ time interpolation: linear
+ obs operator:
+ name: Identity
+ observation alias file: ./obsop_name_map.yaml
+ obs error:
+ covariance model: diagonal
+ obs filters:
+ - filter: Perform Action
+ action:
+ name: assign error
+ error function:
+ name: ObsFunction/LinearCombination
+ options:
+ variables:
+ - ObsError/seaSurfaceSalinity
+ coefs:
+ - 1000.0
+{% if marine_letkf_app | default(false) %}
+ obs localizations:
+ - localization method: Rossby
+ base value: 100.0e3
+ rossby mult: 1.0
+ min grid mult: 2.0
+ min value: 200.0e3
+ max value: 900.0e3
+{% endif %}
diff --git a/parm/jcb-gdas/observations/marine/insitu_temp_profile_argo.yaml.j2 b/parm/jcb-gdas/observations/marine/insitu_temp_profile_argo.yaml.j2
new file mode 100644
index 000000000..b2c0572e1
--- /dev/null
+++ b/parm/jcb-gdas/observations/marine/insitu_temp_profile_argo.yaml.j2
@@ -0,0 +1,198 @@
+- obs space:
+ name: {{observation_from_jcb}}
+ obsdatain:
+ engine:
+ type: H5File
+ obsfile: "{{marine_obsdatain_path}}/{{marine_obsdatain_prefix}}{{observation_from_jcb}}{{marine_obsdatain_suffix}}"
+ missing file action: warn
+ obsgrouping:
+ group variables: [latitude, longitude, dateTime]
+ sort variable: depth
+ sort group: MetaData
+ sort order: ascending
+ obsdataout:
+ engine:
+ type: H5File
+ obsfile: "{{marine_obsdataout_path}}/{{marine_obsdataout_prefix}}{{observation_from_jcb}}{{marine_obsdataout_suffix}}"
+ simulated variables: [waterTemperature]
+ observed variables: [waterTemperature]
+ io pool:
+ max pool size: 1
+{% if marine_letkf_app | default(false) %}
+ distribution:
+ name: Halo
+ halo size: {{ marine_letkf_dist_halo_size }}
+{% endif %}
+ obs operator:
+ name: InsituTemperature
+ obs error:
+ covariance model: diagonal
+
+ #-------------------------------------------------------------------------------
+ # START OF OBS FILTERS (work done by Kriti Bhargava)
+ # The QC filters used here are based on the document by IODE that can be found at
+ # https://cdn.ioos.noaa.gov/media/2017/12/recommendations_in_situ_data_real_time_qc.pdf
+ #-------------------------------------------------------------------------------
+
+ obs filters:
+
+ # land check
+ - filter: Domain Check
+ where:
+ - variable: {name: GeoVaLs/sea_area_fraction}
+ value: is_valid
+ minvalue: 0.5
+
+ #-------------------------------------------------------------------------------
+ ## Filters for T:
+ #-------------------------------------------------------------------------------
+ #-------------------------------------------------------------------------------
+ ### Global range test
+ #-----------------------------------------------------------------------------
+
+ - filter: Bounds Check
+ filter variables: [{name: waterTemperature}]
+ minvalue: -2.5
+ maxvalue: 40.0
+
+ #-----------------------------------------------------------------------------
+ ### Regional range tests
+ #-----------------------------------------------------------------------------
+
+ #### Red Sea
+ #-----------------------------------------------------------------------------
+ ####
+ #### the document linked here describes Red sea as the are between 10N, 40E;
+ #### 20N, 50E; 30N, 30E; 10N, 40E. But that would also include Gulf of Aden.
+ #### A more reasonable choice seemed to be a box that extends from 10 N to
+ #### 30 N and 30 E to 45 East .
+
+ - filter: Bounds Check
+ filter variables: [{name: waterTemperature}]
+ minvalue: 21.7
+ maxvalue: 40.0
+ where:
+ - variable:
+ name: MetaData/latitude
+ minvalue: 10
+ maxvalue: 30
+ - variable:
+ name: MetaData/longitude
+ minvalue: 30
+ maxvalue: 45
+
+ #### Mediterranean Sea
+ #-----------------------------------------------------------------------------
+ ##### Area 1/3 for Mediterranean Sea
+ - filter: Bounds Check
+ filter variables: [{name: waterTemperature}]
+ minvalue: 10.0
+ maxvalue: 40.0
+ where:
+ - variable:
+ name: MetaData/latitude
+ minvalue: 30
+ maxvalue: 40
+ - variable:
+ name: MetaData/longitude
+ minvalue: -6
+ maxvalue: 40
+ ##### Area 2/3 for Mediterranean Sea
+ - filter: Bounds Check
+ filter variables: [{name: waterTemperature}]
+ minvalue: 10.0
+ maxvalue: 40.0
+ where:
+ - variable:
+ name: MetaData/latitude
+ minvalue: 40
+ maxvalue: 41.5
+ - variable:
+ name: MetaData/longitude
+ minvalue: 20
+ maxvalue: 30
+ ##### Area 3/3 for Mediterranean Sea
+ - filter: Bounds Check
+ filter variables: [{name: waterTemperature}]
+ minvalue: 10.0
+ maxvalue: 40.0
+ where:
+ - variable:
+ name: MetaData/latitude
+ minvalue: 40
+ maxvalue: 46
+ - variable:
+ name: MetaData/longitude
+ minvalue: 0
+ maxvalue: 20
+
+ #### Northwestern shelves
+ #-----------------------------------------------------------------------------
+
+ - filter: Bounds Check
+ filter variables: [{name: waterTemperature}]
+ minvalue: -2.0
+ maxvalue: 24.0
+ where:
+ - variable:
+ name: MetaData/latitude
+ minvalue: 50
+ maxvalue: 60
+ - variable:
+ name: MetaData/longitude
+ minvalue: -20
+ maxvalue: 10
+
+ #### Southwestern shelves
+ #-----------------------------------------------------------------------------
+
+ - filter: Bounds Check
+ filter variables: [{name: waterTemperature}]
+ minvalue: -2.0
+ maxvalue: 30
+ where:
+ - variable:
+ name: MetaData/latitude
+ minvalue: 25
+ maxvalue: 50
+ - variable:
+ name: MetaData/longitude
+ minvalue: -30
+ maxvalue: 0
+
+ #### Arctic Ocean
+ #-----------------------------------------------------------------------------
+
+ - filter: Bounds Check
+ filter variables: [{name: waterTemperature}]
+ minvalue: -1.92
+ maxvalue: 25.0
+ where:
+ - variable:
+ name: MetaData/latitude
+ minvalue: 60
+
+# - filter: Background Check
+# filter variables: [{name: waterTemperature}]
+# threshold: 5.0
+# absolute threshold: 5.0
+
+ - filter: Perform Action
+ action:
+ name: assign error
+ error function:
+ name: ObsFunction/LinearCombination
+ options:
+ variables:
+ - ObsError/waterTemperature
+ coefs:
+ - 100.0
+{% if marine_letkf_app | default(false) %}
+ obs localizations:
+ - localization method: Rossby
+ base value: 100.0e3
+ rossby mult: 1.0
+ min grid mult: 2.0
+ min value: 200.0e3
+ max value: 900.0e3
+{% endif %}
diff --git a/parm/jcb-gdas/observations/marine/insitu_temp_surface_drifter.yaml.j2 b/parm/jcb-gdas/observations/marine/insitu_temp_surface_drifter.yaml.j2
new file mode 100644
index 000000000..648ee2ed8
--- /dev/null
+++ b/parm/jcb-gdas/observations/marine/insitu_temp_surface_drifter.yaml.j2
@@ -0,0 +1,65 @@
+- obs space:
+ name: {{observation_from_jcb}}
+ obsdatain:
+ engine:
+ type: H5File
+ obsfile: "{{marine_obsdatain_path}}/{{marine_obsdatain_prefix}}{{observation_from_jcb}}{{marine_obsdatain_suffix}}"
+ missing file action: warn
+ obsdataout:
+ engine:
+ type: H5File
+ obsfile: "{{marine_obsdataout_path}}/{{marine_obsdataout_prefix}}{{observation_from_jcb}}{{marine_obsdataout_suffix}}"
+ simulated variables: [seaSurfaceTemperature]
+ observed variables: [seaSurfaceTemperature]
+ io pool:
+ max pool size: 1
+{% if marine_letkf_app | default(false) %}
+ distribution:
+ name: Halo
+ halo size: {{ marine_letkf_dist_halo_size }}
+{% endif %}
+ get values:
+ time interpolation: linear
+ obs operator:
+ name: Identity
+ observation alias file: obsop_name_map.yaml
+ obs error:
+ covariance model: diagonal
+
+ obs pre filters:
+ - filter: Bounds Check
+ minvalue: -1.2
+ maxvalue: 41.0
+ - filter: Domain Check
+ where:
+ - variable: {name: ObsError/seaSurfaceTemperature}
+ minvalue: 1.0e-8
+
+ obs prior filters:
+ - filter: Domain Check
+ where:
+ - variable: {name: GeoVaLs/sea_area_fraction}
+ value: is_valid
+ minvalue: 0.9
+ - filter: Domain Check
+ where:
+ - variable: { name: GeoVaLs/sea_ice_area_fraction}
+ maxvalue: 1.0e-5
+ - filter: Domain Check
+ where:
+ - variable: {name: GeoVaLs/sea_surface_temperature}
+ minvalue: -1.2
+
+ obs post filters:
+ - filter: Background Check
+ absolute threshold: 5.0
+
+{% if marine_letkf_app | default(false) %}
+ obs localizations:
+ - localization method: Rossby
+ base value: 100.0e3
+ rossby mult: 1.0
+ min grid mult: 2.0
+ min value: 200.0e3
+ max value: 900.0e3
+{% endif %}
diff --git a/parm/jcb-gdas/observations/marine/rads_adt_3a.yaml.j2 b/parm/jcb-gdas/observations/marine/rads_adt_3a.yaml.j2
new file mode 120000
index 000000000..02ad0a9d7
--- /dev/null
+++ b/parm/jcb-gdas/observations/marine/rads_adt_3a.yaml.j2
@@ -0,0 +1 @@
+adt_rads_all.yaml.j2
\ No newline at end of file
diff --git a/parm/jcb-gdas/observations/marine/rads_adt_3b.yaml.j2 b/parm/jcb-gdas/observations/marine/rads_adt_3b.yaml.j2
new file mode 120000
index 000000000..02ad0a9d7
--- /dev/null
+++ b/parm/jcb-gdas/observations/marine/rads_adt_3b.yaml.j2
@@ -0,0 +1 @@
+adt_rads_all.yaml.j2
\ No newline at end of file
diff --git a/parm/jcb-gdas/observations/marine/rads_adt_6a.yaml.j2 b/parm/jcb-gdas/observations/marine/rads_adt_6a.yaml.j2
new file mode 120000
index 000000000..02ad0a9d7
--- /dev/null
+++ b/parm/jcb-gdas/observations/marine/rads_adt_6a.yaml.j2
@@ -0,0 +1 @@
+adt_rads_all.yaml.j2
\ No newline at end of file
diff --git a/parm/jcb-gdas/observations/marine/rads_adt_c2.yaml.j2 b/parm/jcb-gdas/observations/marine/rads_adt_c2.yaml.j2
new file mode 120000
index 000000000..02ad0a9d7
--- /dev/null
+++ b/parm/jcb-gdas/observations/marine/rads_adt_c2.yaml.j2
@@ -0,0 +1 @@
+adt_rads_all.yaml.j2
\ No newline at end of file
diff --git a/parm/jcb-gdas/observations/marine/rads_adt_j2.yaml.j2 b/parm/jcb-gdas/observations/marine/rads_adt_j2.yaml.j2
new file mode 120000
index 000000000..02ad0a9d7
--- /dev/null
+++ b/parm/jcb-gdas/observations/marine/rads_adt_j2.yaml.j2
@@ -0,0 +1 @@
+adt_rads_all.yaml.j2
\ No newline at end of file
diff --git a/parm/jcb-gdas/observations/marine/rads_adt_j3.yaml.j2 b/parm/jcb-gdas/observations/marine/rads_adt_j3.yaml.j2
new file mode 120000
index 000000000..02ad0a9d7
--- /dev/null
+++ b/parm/jcb-gdas/observations/marine/rads_adt_j3.yaml.j2
@@ -0,0 +1 @@
+adt_rads_all.yaml.j2
\ No newline at end of file
diff --git a/parm/jcb-gdas/observations/marine/rads_adt_sa.yaml.j2 b/parm/jcb-gdas/observations/marine/rads_adt_sa.yaml.j2
new file mode 120000
index 000000000..02ad0a9d7
--- /dev/null
+++ b/parm/jcb-gdas/observations/marine/rads_adt_sa.yaml.j2
@@ -0,0 +1 @@
+adt_rads_all.yaml.j2
\ No newline at end of file
diff --git a/parm/jcb-gdas/observations/marine/rads_adt_sw.yaml.j2 b/parm/jcb-gdas/observations/marine/rads_adt_sw.yaml.j2
new file mode 120000
index 000000000..02ad0a9d7
--- /dev/null
+++ b/parm/jcb-gdas/observations/marine/rads_adt_sw.yaml.j2
@@ -0,0 +1 @@
+adt_rads_all.yaml.j2
\ No newline at end of file
diff --git a/parm/jcb-gdas/observations/marine/sss_smap_l2.yaml.j2 b/parm/jcb-gdas/observations/marine/sss_smap_l2.yaml.j2
new file mode 100644
index 000000000..a075b5545
--- /dev/null
+++ b/parm/jcb-gdas/observations/marine/sss_smap_l2.yaml.j2
@@ -0,0 +1,60 @@
+- obs space:
+ name: {{observation_from_jcb}}
+ obsdatain:
+ engine:
+ type: H5File
+ obsfile: "{{marine_obsdatain_path}}/{{marine_obsdatain_prefix}}{{observation_from_jcb}}{{marine_obsdatain_suffix}}"
+ missing file action: warn
+ obsdataout:
+ engine:
+ type: H5File
+ obsfile: "{{marine_obsdataout_path}}/{{marine_obsdataout_prefix}}{{observation_from_jcb}}{{marine_obsdataout_suffix}}"
+ simulated variables: [seaSurfaceSalinity]
+ io pool:
+ max pool size: 1
+{% if marine_letkf_app | default(false) %}
+ distribution:
+ name: Halo
+ halo size: {{ marine_letkf_dist_halo_size }}
+{% endif %}
+ get values:
+ time interpolation: linear
+ obs operator:
+ name: Identity
+ observation alias file: obsop_name_map.yaml
+ obs error:
+ covariance model: diagonal
+ obs filters:
+ - filter: Domain Check
+ where:
+ - variable: {name: GeoVaLs/sea_area_fraction}
+ value: is_valid
+ minvalue: 0.9
+ - filter: Bounds Check
+ minvalue: 0.1
+ maxvalue: 40.0
+ - filter: Background Check
+ threshold: 5.0
+ - filter: Domain Check
+ action:
+ name: passivate
+ where:
+ - variable: {name: GeoVaLs/sea_surface_temperature}
+# minvalue: 15.0
+ maxvalue: -4.0
+ ## Gaussian_Thinning is having problems with LETKF, try again later
+ # - filter: Gaussian_Thinning
+ # horizontal_mesh: 25.0 #km
+ - filter: Domain Check
+ where:
+ - variable: {name: GeoVaLs/distance_from_coast}
+ minvalue: 100e3
+{% if marine_letkf_app | default(false) %}
+ obs localizations:
+ - localization method: Rossby
+ base value: 100.0e3
+ rossby mult: 1.0
+ min grid mult: 2.0
+ min value: 200.0e3
+ max value: 900.0e3
+{% endif %}
diff --git a/parm/jcb-gdas/observations/marine/sss_smos_l2.yaml.j2 b/parm/jcb-gdas/observations/marine/sss_smos_l2.yaml.j2
new file mode 100644
index 000000000..a075b5545
--- /dev/null
+++ b/parm/jcb-gdas/observations/marine/sss_smos_l2.yaml.j2
@@ -0,0 +1,60 @@
+- obs space:
+ name: {{observation_from_jcb}}
+ obsdatain:
+ engine:
+ type: H5File
+ obsfile: "{{marine_obsdatain_path}}/{{marine_obsdatain_prefix}}{{observation_from_jcb}}{{marine_obsdatain_suffix}}"
+ missing file action: warn
+ obsdataout:
+ engine:
+ type: H5File
+ obsfile: "{{marine_obsdataout_path}}/{{marine_obsdataout_prefix}}{{observation_from_jcb}}{{marine_obsdataout_suffix}}"
+ simulated variables: [seaSurfaceSalinity]
+ io pool:
+ max pool size: 1
+{% if marine_letkf_app | default(false) %}
+ distribution:
+ name: Halo
+ halo size: {{ marine_letkf_dist_halo_size }}
+{% endif %}
+ get values:
+ time interpolation: linear
+ obs operator:
+ name: Identity
+ observation alias file: obsop_name_map.yaml
+ obs error:
+ covariance model: diagonal
+ obs filters:
+ - filter: Domain Check
+ where:
+ - variable: {name: GeoVaLs/sea_area_fraction}
+ value: is_valid
+ minvalue: 0.9
+ - filter: Bounds Check
+ minvalue: 0.1
+ maxvalue: 40.0
+ - filter: Background Check
+ threshold: 5.0
+ - filter: Domain Check
+ action:
+ name: passivate
+ where:
+ - variable: {name: GeoVaLs/sea_surface_temperature}
+# minvalue: 15.0
+ maxvalue: -4.0
+ ## Gaussian_Thinning is having problems with LETKF, try again later
+ # - filter: Gaussian_Thinning
+ # horizontal_mesh: 25.0 #km
+ - filter: Domain Check
+ where:
+ - variable: {name: GeoVaLs/distance_from_coast}
+ minvalue: 100e3
+{% if marine_letkf_app | default(false) %}
+ obs localizations:
+ - localization method: Rossby
+ base value: 100.0e3
+ rossby mult: 1.0
+ min grid mult: 2.0
+ min value: 200.0e3
+ max value: 900.0e3
+{% endif %}
diff --git a/parm/jcb-gdas/observations/marine/sst_abi_g16_l3c.yaml.j2 b/parm/jcb-gdas/observations/marine/sst_abi_g16_l3c.yaml.j2
new file mode 120000
index 000000000..b3649a670
--- /dev/null
+++ b/parm/jcb-gdas/observations/marine/sst_abi_g16_l3c.yaml.j2
@@ -0,0 +1 @@
+sst_generic_geo.yaml.j2
\ No newline at end of file
diff --git a/parm/jcb-gdas/observations/marine/sst_abi_g17_l3c.yaml.j2 b/parm/jcb-gdas/observations/marine/sst_abi_g17_l3c.yaml.j2
new file mode 120000
index 000000000..b3649a670
--- /dev/null
+++ b/parm/jcb-gdas/observations/marine/sst_abi_g17_l3c.yaml.j2
@@ -0,0 +1 @@
+sst_generic_geo.yaml.j2
\ No newline at end of file
diff --git a/parm/jcb-gdas/observations/marine/sst_ahi_h08_l3c.yaml.j2 b/parm/jcb-gdas/observations/marine/sst_ahi_h08_l3c.yaml.j2
new file mode 120000
index 000000000..b3649a670
--- /dev/null
+++ b/parm/jcb-gdas/observations/marine/sst_ahi_h08_l3c.yaml.j2
@@ -0,0 +1 @@
+sst_generic_geo.yaml.j2
\ No newline at end of file
diff --git a/parm/jcb-gdas/observations/marine/sst_avhrr_ma_l3u.yaml.j2 b/parm/jcb-gdas/observations/marine/sst_avhrr_ma_l3u.yaml.j2
new file mode 120000
index 000000000..5298b9a81
--- /dev/null
+++ b/parm/jcb-gdas/observations/marine/sst_avhrr_ma_l3u.yaml.j2
@@ -0,0 +1 @@
+sst_generic.yaml.j2
\ No newline at end of file
diff --git a/parm/jcb-gdas/observations/marine/sst_avhrr_mb_l3u.yaml.j2 b/parm/jcb-gdas/observations/marine/sst_avhrr_mb_l3u.yaml.j2
new file mode 120000
index 000000000..5298b9a81
--- /dev/null
+++ b/parm/jcb-gdas/observations/marine/sst_avhrr_mb_l3u.yaml.j2
@@ -0,0 +1 @@
+sst_generic.yaml.j2
\ No newline at end of file
diff --git a/parm/jcb-gdas/observations/marine/sst_avhrr_mc_l3u.yaml.j2 b/parm/jcb-gdas/observations/marine/sst_avhrr_mc_l3u.yaml.j2
new file mode 120000
index 000000000..5298b9a81
--- /dev/null
+++ b/parm/jcb-gdas/observations/marine/sst_avhrr_mc_l3u.yaml.j2
@@ -0,0 +1 @@
+sst_generic.yaml.j2
\ No newline at end of file
diff --git a/parm/jcb-gdas/observations/marine/sst_avhrrf_ma_l3u.yaml.j2 b/parm/jcb-gdas/observations/marine/sst_avhrrf_ma_l3u.yaml.j2
new file mode 120000
index 000000000..5298b9a81
--- /dev/null
+++ b/parm/jcb-gdas/observations/marine/sst_avhrrf_ma_l3u.yaml.j2
@@ -0,0 +1 @@
+sst_generic.yaml.j2
\ No newline at end of file
diff --git a/parm/jcb-gdas/observations/marine/sst_avhrrf_mb_l3u.yaml.j2 b/parm/jcb-gdas/observations/marine/sst_avhrrf_mb_l3u.yaml.j2
new file mode 120000
index 000000000..5298b9a81
--- /dev/null
+++ b/parm/jcb-gdas/observations/marine/sst_avhrrf_mb_l3u.yaml.j2
@@ -0,0 +1 @@
+sst_generic.yaml.j2
\ No newline at end of file
diff --git a/parm/jcb-gdas/observations/marine/sst_avhrrf_mc_l3u.yaml.j2 b/parm/jcb-gdas/observations/marine/sst_avhrrf_mc_l3u.yaml.j2
new file mode 120000
index 000000000..5298b9a81
--- /dev/null
+++ b/parm/jcb-gdas/observations/marine/sst_avhrrf_mc_l3u.yaml.j2
@@ -0,0 +1 @@
+sst_generic.yaml.j2
\ No newline at end of file
diff --git a/parm/jcb-gdas/observations/marine/sst_generic.yaml.j2 b/parm/jcb-gdas/observations/marine/sst_generic.yaml.j2
new file mode 100644
index 000000000..d887bf220
--- /dev/null
+++ b/parm/jcb-gdas/observations/marine/sst_generic.yaml.j2
@@ -0,0 +1,78 @@
+- obs space:
+ name: {{observation_from_jcb}}
+ obsdatain:
+ engine:
+ type: H5File
+ obsfile: "{{marine_obsdatain_path}}/{{marine_obsdatain_prefix}}{{observation_from_jcb}}{{marine_obsdatain_suffix}}"
+ missing file action: warn
+ obsdataout:
+ engine:
+ type: H5File
+ obsfile: "{{marine_obsdataout_path}}/{{marine_obsdataout_prefix}}{{observation_from_jcb}}{{marine_obsdataout_suffix}}"
+ simulated variables: [seaSurfaceTemperature]
+ io pool:
+ max pool size: 1
+{% if marine_letkf_app | default(false) %}
+ distribution:
+ name: Halo
+ halo size: {{ marine_letkf_dist_halo_size }}
+{% endif %}
+ get values:
+ time interpolation: linear
+ obs operator:
+ name: Identity
+ observation alias file: obsop_name_map.yaml
+ obs error:
+ covariance model: diagonal
+
+ obs prior filters:
+ - filter: Domain Check
+ where:
+ - variable: {name: GeoVaLs/distance_from_coast}
+ minvalue: 50e3
+ - filter: Perform Action # accept obs that failed previous QC in Pamlico Sound & Chesapeake Bay
+ action:
+ name: accept
+ where:
+ - variable:
+ name: MetaData/latitude
+ minvalue: 34.5
+ maxvalue: 39.7
+ - variable:
+ name: MetaData/longitude
+ minvalue: -76.88
+ maxvalue: -74.5
+ - filter: Bounds Check
+ minvalue: -1.2
+ maxvalue: 41.0
+ - filter: Domain Check
+ where:
+ - variable: {name: ObsError/seaSurfaceTemperature}
+ minvalue: 1.0e-8
+ - filter: Domain Check
+ where:
+ - variable: {name: GeoVaLs/sea_area_fraction}
+ value: is_valid
+ minvalue: 0.9
+ - filter: Domain Check
+ where:
+ - variable: { name: GeoVaLs/sea_ice_area_fraction}
+ maxvalue: 1.0e-5
+ - filter: Domain Check
+ where:
+ - variable: {name: GeoVaLs/sea_surface_temperature}
+ minvalue: -1.2
+
+ obs post filters:
+ - filter: Background Check
+ absolute threshold: 5.0
+
+{% if marine_letkf_app | default(false) %}
+ obs localizations:
+ - localization method: Rossby
+ base value: 100.0e3
+ rossby mult: 1.0
+ min grid mult: 2.0
+ min value: 200.0e3
+ max value: 900.0e3
+{% endif %}
diff --git a/parm/jcb-gdas/observations/marine/sst_generic_geo.yaml.j2 b/parm/jcb-gdas/observations/marine/sst_generic_geo.yaml.j2
new file mode 100644
index 000000000..ffe625a4e
--- /dev/null
+++ b/parm/jcb-gdas/observations/marine/sst_generic_geo.yaml.j2
@@ -0,0 +1,84 @@
+- obs space:
+ name: {{observation_from_jcb}}
+ obsdatain:
+ engine:
+ type: H5File
+ obsfile: "{{marine_obsdatain_path}}/{{marine_obsdatain_prefix}}{{observation_from_jcb}}{{marine_obsdatain_suffix}}"
+ missing file action: warn
+ obsdataout:
+ engine:
+ type: H5File
+ obsfile: "{{marine_obsdataout_path}}/{{marine_obsdataout_prefix}}{{observation_from_jcb}}{{marine_obsdataout_suffix}}"
+ simulated variables: [seaSurfaceTemperature]
+ io pool:
+ max pool size: 1
+{% if marine_letkf_app | default(false) %}
+ distribution:
+ name: Halo
+ halo size: {{ marine_letkf_dist_halo_size }}
+{% endif %}
+ get values:
+ time interpolation: linear
+ obs operator:
+ name: Identity
+ observation alias file: obsop_name_map.yaml
+ obs error:
+ covariance model: diagonal
+
+ obs prior filters:
+ - filter: Domain Check
+ where:
+ - variable: {name: GeoVaLs/distance_from_coast}
+ minvalue: 50e3
+ - filter: Perform Action # accept obs that failed previous QC in Pamlico Sound & Chesapeake Bay
+ action:
+ name: accept
+ where:
+ - variable:
+ name: MetaData/latitude
+ minvalue: 34.5
+ maxvalue: 39.7
+ - variable:
+ name: MetaData/longitude
+ minvalue: -76.88
+ maxvalue: -74.5
+ - filter: Bounds Check
+ minvalue: -1.2
+ maxvalue: 41.0
+ - filter: Domain Check
+ where:
+ - variable: {name: ObsError/seaSurfaceTemperature}
+ minvalue: 1.0e-8
+ - filter: Domain Check
+ where:
+ - variable: {name: GeoVaLs/sea_area_fraction}
+ value: is_valid
+ minvalue: 0.9
+ - filter: Domain Check
+ where:
+ - variable: { name: GeoVaLs/sea_ice_area_fraction}
+ maxvalue: 1.0e-5
+ - filter: Domain Check
+ where:
+ - variable: {name: GeoVaLs/sea_surface_temperature}
+ minvalue: -1.2
+ - filter: Domain Check
+ action:
+ name: passivate
+ where:
+ - variable: {name: GeoVaLs/sea_surface_temperature}
+ maxvalue: -4.0
+
+ obs post filters:
+ - filter: Background Check
+ absolute threshold: 5.0
+
+{% if marine_letkf_app | default(false) %}
+ obs localizations:
+ - localization method: Rossby
+ base value: 100.0e3
+ rossby mult: 1.0
+ min grid mult: 2.0
+ min value: 200.0e3
+ max value: 900.0e3
+{% endif %}
diff --git a/parm/jcb-gdas/observations/marine/sst_viirs_n20_l3u.yaml.j2 b/parm/jcb-gdas/observations/marine/sst_viirs_n20_l3u.yaml.j2
new file mode 120000
index 000000000..5298b9a81
--- /dev/null
+++ b/parm/jcb-gdas/observations/marine/sst_viirs_n20_l3u.yaml.j2
@@ -0,0 +1 @@
+sst_generic.yaml.j2
\ No newline at end of file
diff --git a/parm/jcb-gdas/observations/marine/sst_viirs_n21_l3u.yaml.j2 b/parm/jcb-gdas/observations/marine/sst_viirs_n21_l3u.yaml.j2
new file mode 120000
index 000000000..5298b9a81
--- /dev/null
+++ b/parm/jcb-gdas/observations/marine/sst_viirs_n21_l3u.yaml.j2
@@ -0,0 +1 @@
+sst_generic.yaml.j2
\ No newline at end of file
diff --git a/parm/jcb-gdas/observations/marine/sst_viirs_npp_l3u.yaml.j2 b/parm/jcb-gdas/observations/marine/sst_viirs_npp_l3u.yaml.j2
new file mode 120000
index 000000000..5298b9a81
--- /dev/null
+++ b/parm/jcb-gdas/observations/marine/sst_viirs_npp_l3u.yaml.j2
@@ -0,0 +1 @@
+sst_generic.yaml.j2
\ No newline at end of file
diff --git a/parm/jcb-gdas/observations/snow/adpsfc_snow.yaml.j2 b/parm/jcb-gdas/observations/snow/adpsfc_snow.yaml.j2
new file mode 100644
index 000000000..cd3aa5f8a
--- /dev/null
+++ b/parm/jcb-gdas/observations/snow/adpsfc_snow.yaml.j2
@@ -0,0 +1,217 @@
+-
+
+ # Observation Space (I/O)
+ # -----------------------
+ obs space:
+ name: {{observation_from_jcb}}
+ obsdatain:
+ engine:
+ type: bufr
+ obsfile: "{{snow_obsdatain_path}}/{{snow_obsdatain_prefix}}{{observation_from_jcb}}{{snow_obsdatain_suffix}}"
+ mapping file: "{{snow_obsdatain_path}}/bufr_adpsfc_mapping.yaml"
+ missing file action: warn
+ obsgrouping:
+ group variables: [stationIdentification]
+ obsdataout:
+ engine:
+ type: H5File
+ obsfile: "{{snow_obsdataout_path}}/{{snow_obsdataout_prefix}}{{observation_from_jcb}}{{snow_obsdataout_suffix}}"
+ simulated variables: [totalSnowDepth]
+ #
+
+ # Observation Operator
+ # --------------------
+ obs operator:
+ name: Identity
+ #
+
+ # Observation Filters (QC)
+ # ------------------------
+ obs pre filters:
+ - filter: Create Diagnostic Flags
+ flags:
+ - name: missing_snowdepth
+ initial value: false
+ - name: missing_elevation
+ initial value: false
+ - name: temporal_thinning
+ initial value: false
+ - name: invalid_snowdepth
+ initial value: false
+ - name: invalid_elevation
+ initial value: false
+ - name: land_check
+ initial value: false
+ - name: landice_check
+ initial value: false
+ - name: seaice_check
+ initial value: false
+ - name: elevation_bkgdiff
+ initial value: false
+ - name: rejectlist
+ initial value: false
+ - name: background_check
+ initial value: false
+ - filter: Perform Action
+ filter variables:
+ - name: totalSnowDepth
+ action:
+ name: assign error
+ error parameter: 40.0
+ - filter: Domain Check
+ where:
+ - variable:
+ name: ObsValue/totalSnowDepth
+ value: is_valid
+ actions:
+ - name: set
+ flag: missing_snowdepth
+ ignore: rejected observations
+ - name: reject
+ - filter: Domain Check
+ where:
+ - variable:
+ name: MetaData/stationElevation
+ value: is_valid
+ actions:
+ - name: set
+ flag: missing_elevation
+ ignore: rejected observations
+ - name: reject
+ - filter: Temporal Thinning
+ min_spacing: '{{ window_length }}'
+ seed_time: '{{ snow_background_time_iso }}'
+ category_variable:
+ name: MetaData/stationIdentification
+ actions:
+ - name: set
+ flag: temporal_thinning
+ ignore: rejected observations
+ - name: reject
+ obs prior filters:
+ - filter: Bounds Check
+ filter variables:
+ - name: totalSnowDepth
+ minvalue: 0.0
+ maxvalue: 20000.0
+ actions:
+ - name: set
+ flag: invalid_snowdepth
+ ignore: rejected observations
+ - name: reject
+ - filter: Domain Check # land only
+ where:
+ - variable:
+ name: GeoVaLs/fraction_of_land
+ minvalue: 0.5
+ actions:
+ - name: set
+ flag: land_check
+ ignore: rejected observations
+ - name: reject
+ - filter: Domain Check
+ where:
+ - variable:
+ name: MetaData/stationElevation
+ minvalue: -200.0
+ maxvalue: 3000.0
+ actions:
+ - name: set
+ flag: invalid_elevation
+ ignore: rejected observations
+ - name: reject
+ - filter: Domain Check # land only, no sea ice
+ where:
+ - variable:
+ name: GeoVaLs/fraction_of_ice
+ maxvalue: 0.0
+ actions:
+ - name: set
+ flag: seaice_check
+ ignore: rejected observations
+ - name: reject
+ - filter: RejectList # no land-ice
+ where:
+ - variable:
+ name: GeoVaLs/vtype
+ minvalue: 14.5
+ maxvalue: 15.5
+ actions:
+ - name: set
+ flag: landice_check
+ ignore: rejected observations
+ - name: reject
+ - filter: Difference Check # elevation check
+ reference: MetaData/stationElevation
+ value: GeoVaLs/filtered_orography
+ threshold: 800.
+ actions:
+ - name: set
+ flag: elevation_bkgdiff
+ ignore: rejected observations
+ - name: reject
+ # Add inflate error characterized by a function of elevation difference
+ - filter: Variable Assignment
+ assignments:
+ - name: DerivedMetaData/elevation_diff
+ type: float
+ function:
+ name: ObsFunction/Arithmetic
+ options:
+ variables: [MetaData/stationElevation, GeoVaLs/filtered_orography]
+ coefficients: [1., -1.]
+ total exponent: 2
+ total coefficient: 0.0000015625 #1/(800*800)
+ - filter: Variable Assignment
+ assignments:
+ - name: DerivedMetaData/elevation_diff_exp
+ type: float
+ function:
+ name: ObsFunction/Exponential
+ options:
+ variables: [DerivedMetaData/elevation_diff]
+ coeffA: 1.
+ coeffB: -1.
+ coeffC: 0.
+ coeffD: 1.
+ - filter: Variable Assignment
+ assignments:
+ - name: DerivedMetaData/elevation_diff_exp_inv
+ type: float
+ function:
+ name: ObsFunction/Arithmetic
+ options:
+ variables: [DerivedMetaData/elevation_diff_exp]
+ total exponent: -1.
+ - filter: Perform Action
+ filter variables:
+ - name: totalSnowDepth
+ where:
+ - variable:
+ name: ObsValue/totalSnowDepth
+ minvalue: 0.
+ action:
+ name: inflate error
+ inflation variable: DerivedMetaData/elevation_diff_exp_inv # 2.0
+ - filter: BlackList
+ where:
+ - variable:
+ name: MetaData/stationIdentification
+ is_in: {{ get_conventional_rejected_stations(observation_from_jcb) }}
+ actions:
+ - name: set
+ flag: rejectlist
+ ignore: rejected observations
+ - name: reject
+ obs post filters:
+ - filter: Background Check # gross error check
+ filter variables:
+ - name: totalSnowDepth
+ absolute threshold: 250
+ bias correction parameter: 1.0
+ actions:
+ - name: set
+ flag: background_check
+ ignore: rejected observations
+ - name: reject
+
diff --git a/parm/jcb-gdas/observations/snow/ghcn_snow.yaml.j2 b/parm/jcb-gdas/observations/snow/ghcn_snow.yaml.j2
new file mode 100644
index 000000000..4ad6a7444
--- /dev/null
+++ b/parm/jcb-gdas/observations/snow/ghcn_snow.yaml.j2
@@ -0,0 +1,202 @@
+-
+
+ # Observation Space (I/O)
+ # -----------------------
+ obs space:
+ name: {{observation_from_jcb}}
+ obsdatain:
+ engine:
+ type: H5File
+ obsfile: "{{snow_prepobs_path}}/{{snow_obsdatain_prefix}}{{observation_from_jcb}}.nc"
+ missing file action: warn
+ obsdataout:
+ engine:
+ type: H5File
+ obsfile: "{{snow_obsdataout_path}}/{{snow_obsdataout_prefix}}{{observation_from_jcb}}{{snow_obsdataout_suffix}}"
+ simulated variables: [totalSnowDepth]
+ #
+
+ # Observation Operator
+ # --------------------
+ obs operator:
+ name: Identity
+ #
+
+ # Observation Filters (QC)
+ # ------------------------
+ obs pre filters:
+ - filter: Create Diagnostic Flags
+ flags:
+ - name: missing_snowdepth
+ initial value: false
+ - name: missing_elevation
+ initial value: false
+ - name: invalid_snowdepth
+ initial value: false
+ - name: invalid_elevation
+ initial value: false
+ - name: land_check
+ initial value: false
+ - name: landice_check
+ initial value: false
+ - name: seaice_check
+ initial value: false
+ - name: elevation_bkgdiff
+ initial value: false
+ - name: rejectlist
+ initial value: false
+ - name: background_check
+ initial value: false
+ - filter: Perform Action
+ filter variables:
+ - name: totalSnowDepth
+ action:
+ name: assign error
+ error parameter: 40.0
+ - filter: Domain Check
+ where:
+ - variable:
+ name: ObsValue/totalSnowDepth
+ value: is_valid
+ actions:
+ - name: set
+ flag: missing_snowdepth
+ ignore: rejected observations
+ - name: reject
+ - filter: Domain Check
+ where:
+ - variable:
+ name: MetaData/stationElevation
+ value: is_valid
+ actions:
+ - name: set
+ flag: missing_elevation
+ ignore: rejected observations
+ - name: reject
+ obs prior filters:
+ - filter: Bounds Check
+ filter variables:
+ - name: totalSnowDepth
+ minvalue: 0.0
+ maxvalue: 20000.0
+ actions:
+ - name: set
+ flag: invalid_snowdepth
+ ignore: rejected observations
+ - name: reject
+ - filter: Domain Check # land only
+ where:
+ - variable:
+ name: GeoVaLs/fraction_of_land
+ minvalue: 0.5
+ actions:
+ - name: set
+ flag: land_check
+ ignore: rejected observations
+ - name: reject
+ - filter: Domain Check
+ where:
+ - variable:
+ name: MetaData/stationElevation
+ minvalue: -200.0
+ maxvalue: 3000.0
+ actions:
+ - name: set
+ flag: invalid_elevation
+ ignore: rejected observations
+ - name: reject
+ - filter: Domain Check # land only, no sea ice
+ where:
+ - variable:
+ name: GeoVaLs/fraction_of_ice
+ maxvalue: 0.0
+ actions:
+ - name: set
+ flag: seaice_check
+ ignore: rejected observations
+ - name: reject
+ - filter: RejectList # no land-ice
+ where:
+ - variable:
+ name: GeoVaLs/vtype
+ minvalue: 14.5
+ maxvalue: 15.5
+ actions:
+ - name: set
+ flag: landice_check
+ ignore: rejected observations
+ - name: reject
+ - filter: Difference Check # elevation check
+ reference: MetaData/stationElevation
+ value: GeoVaLs/filtered_orography
+ threshold: 800.
+ actions:
+ - name: set
+ flag: elevation_bkgdiff
+ ignore: rejected observations
+ - name: reject
+ # Add inflate error characterized by a function of elevation difference
+ - filter: Variable Assignment
+ assignments:
+ - name: DerivedMetaData/elevation_diff
+ type: float
+ function:
+ name: ObsFunction/Arithmetic
+ options:
+ variables: [MetaData/stationElevation, GeoVaLs/filtered_orography]
+ coefficients: [1., -1.]
+ total exponent: 2
+ total coefficient: 0.0000015625 #1/(800*800)
+ - filter: Variable Assignment
+ assignments:
+ - name: DerivedMetaData/elevation_diff_exp
+ type: float
+ function:
+ name: ObsFunction/Exponential
+ options:
+ variables: [DerivedMetaData/elevation_diff]
+ coeffA: 1.
+ coeffB: -1.
+ coeffC: 0.
+ coeffD: 1.
+ - filter: Variable Assignment
+ assignments:
+ - name: DerivedMetaData/elevation_diff_exp_inv
+ type: float
+ function:
+ name: ObsFunction/Arithmetic
+ options:
+ variables: [DerivedMetaData/elevation_diff_exp]
+ total exponent: -1.
+ - filter: Perform Action
+ filter variables:
+ - name: totalSnowDepth
+ where:
+ - variable:
+ name: ObsValue/totalSnowDepth
+ minvalue: 0.
+ action:
+ name: inflate error
+ inflation variable: DerivedMetaData/elevation_diff_exp_inv # 2.0
+ - filter: BlackList
+ where:
+ - variable:
+ name: MetaData/stationIdentification
+ is_in: {{ get_conventional_rejected_stations(observation_from_jcb) }}
+ actions:
+ - name: set
+ flag: rejectlist
+ ignore: rejected observations
+ - name: reject
+ obs post filters:
+ - filter: Background Check # gross error check
+ filter variables:
+ - name: totalSnowDepth
+ absolute threshold: 250
+ bias correction parameter: 1.0
+ actions:
+ - name: set
+ flag: background_check
+ ignore: rejected observations
+ - name: reject
+
diff --git a/parm/jcb-gdas/observations/snow/ims_snow.yaml.j2 b/parm/jcb-gdas/observations/snow/ims_snow.yaml.j2
new file mode 100644
index 000000000..ef1685c3e
--- /dev/null
+++ b/parm/jcb-gdas/observations/snow/ims_snow.yaml.j2
@@ -0,0 +1,128 @@
+-
+
+ # Observation Space (I/O)
+ # -----------------------
+ obs space:
+ name: {{observation_from_jcb}}
+ obsdatain:
+ engine:
+ type: H5File
+ obsfile: "{{snow_obsdatain_path}}/{{snow_obsdatain_prefix}}{{observation_from_jcb}}.tm00.nc"
+ missing file action: warn
+ obsdataout:
+ engine:
+ type: H5File
+ obsfile: "{{snow_obsdataout_path}}/{{snow_obsdataout_prefix}}{{observation_from_jcb}}{{snow_obsdataout_suffix}}"
+ simulated variables: [totalSnowDepth]
+ #
+
+ # Observation Operator
+ # --------------------
+ obs operator:
+ name: Identity
+ #
+
+ # Observation Filters (QC)
+ # ------------------------
+ obs pre filters:
+ - filter: Create Diagnostic Flags
+ flags:
+ - name: land_check
+ initial value: false
+ - name: landice_check
+ initial value: false
+ - name: seaice_check
+ initial value: false
+ - name: invalid_snowdepth
+ initial value: false
+ - name: invalid_elevation
+ initial value: false
+ - name: background_check
+ initial value: false
+ - name: spatial_thinning
+ initial value: false
+ # assign observation error
+ - filter: Perform Action
+ filter variables:
+ - name: totalSnowDepth
+ action:
+ name: assign error
+ error parameter: 80.0
+
+ obs prior filters:
+ # remove land-ice and sea points
+ - filter: Domain Check # land only
+ where:
+ - variable:
+ name: GeoVaLs/fraction_of_land
+ minvalue: 0.5
+ actions:
+ - name: set
+ flag: land_check
+ ignore: rejected observations
+ - name: reject
+ - filter: Domain Check
+ where:
+ - variable:
+ name: MetaData/stationElevation
+ minvalue: -200.0
+ maxvalue: 3000.0
+ actions:
+ - name: set
+ flag: invalid_elevation
+ ignore: rejected observations
+ - name: reject
+ - filter: Domain Check # land only, no sea ice
+ where:
+ - variable:
+ name: GeoVaLs/fraction_of_ice
+ maxvalue: 0.0
+ actions:
+ - name: set
+ flag: seaice_check
+ ignore: rejected observations
+ - name: reject
+ - filter: RejectList # no land-ice
+ where:
+ - variable:
+ name: GeoVaLs/vtype
+ minvalue: 14.5
+ maxvalue: 15.5
+ actions:
+ - name: set
+ flag: landice_check
+ ignore: rejected observations
+ - name: reject
+
+ obs post filters:
+ # gross error check
+ - filter: Background Check
+ filter variables:
+ - name: totalSnowDepth
+ absolute threshold: 250
+ actions:
+ - name: set
+ flag: background_check
+ ignore: rejected observations
+ - name: reject
+
+ # thinning of remaining obs
+ - filter: Gaussian Thinning
+ horizontal_mesh: 40.0 # km
+ actions:
+ - name: set
+ flag: spatial_thinning
+ ignore: rejected observations
+ - name: reject
+
+ # excludes where both obs & mod = 100% (set in IMS_proc)
+ - filter: Bounds Check
+ filter variables:
+ - name: totalSnowDepth
+ minvalue: 0.0
+ actions:
+ - name: set
+ flag: invalid_snowdepth
+ ignore: rejected observations
+ - name: reject
+
diff --git a/parm/jcb-gdas/observations/snow/madis_snow.yaml.j2 b/parm/jcb-gdas/observations/snow/madis_snow.yaml.j2
new file mode 100644
index 000000000..b900fd37b
--- /dev/null
+++ b/parm/jcb-gdas/observations/snow/madis_snow.yaml.j2
@@ -0,0 +1,216 @@
+-
+
+ # Observation Space (I/O)
+ # -----------------------
+ obs space:
+ name: {{observation_from_jcb}}
+ obsdatain:
+ engine:
+ type: H5File
+ obsfile: "{{snow_obsdatain_path}}/{{snow_obsdatain_prefix}}snocvr_snow.nc4"
+ missing file action: warn
+ obsgrouping:
+ group variables: [stationIdentification]
+ obsdataout:
+ engine:
+ type: H5File
+ obsfile: "{{snow_obsdataout_path}}/{{snow_obsdataout_prefix}}{{observation_from_jcb}}{{snow_obsdataout_suffix}}"
+ simulated variables: [totalSnowDepth]
+ #
+
+ # Observation Operator
+ # --------------------
+ obs operator:
+ name: Identity
+ #
+
+ # Observation Filters (QC)
+ # ------------------------
+ obs pre filters:
+ - filter: Create Diagnostic Flags
+ flags:
+ - name: missing_snowdepth
+ initial value: false
+ - name: missing_elevation
+ initial value: false
+ - name: temporal_thinning
+ initial value: false
+ - name: invalid_snowdepth
+ initial value: false
+ - name: invalid_elevation
+ initial value: false
+ - name: land_check
+ initial value: false
+ - name: landice_check
+ initial value: false
+ - name: seaice_check
+ initial value: false
+ - name: elevation_bkgdiff
+ initial value: false
+ - name: rejectlist
+ initial value: false
+ - name: background_check
+ initial value: false
+ - filter: Perform Action
+ filter variables:
+ - name: totalSnowDepth
+ action:
+ name: assign error
+ error parameter: 40.0
+ - filter: Domain Check
+ where:
+ - variable:
+ name: ObsValue/totalSnowDepth
+ value: is_valid
+ actions:
+ - name: set
+ flag: missing_snowdepth
+ ignore: rejected observations
+ - name: reject
+ - filter: Domain Check
+ where:
+ - variable:
+ name: MetaData/stationElevation
+ value: is_valid
+ actions:
+ - name: set
+ flag: missing_elevation
+ ignore: rejected observations
+ - name: reject
+ - filter: Temporal Thinning
+ min_spacing: '{{ window_length }}'
+ seed_time: '{{ snow_background_time_iso }}'
+ category_variable:
+ name: MetaData/stationIdentification
+ actions:
+ - name: set
+ flag: temporal_thinning
+ ignore: rejected observations
+ - name: reject
+ obs prior filters:
+ - filter: Bounds Check
+ filter variables:
+ - name: totalSnowDepth
+ minvalue: 0.0
+ maxvalue: 20000.0
+ actions:
+ - name: set
+ flag: invalid_snowdepth
+ ignore: rejected observations
+ - name: reject
+ - filter: Domain Check # land only
+ where:
+ - variable:
+ name: GeoVaLs/fraction_of_land
+ minvalue: 0.5
+ actions:
+ - name: set
+ flag: land_check
+ ignore: rejected observations
+ - name: reject
+ - filter: Domain Check
+ where:
+ - variable:
+ name: MetaData/stationElevation
+ minvalue: -200.0
+ maxvalue: 3000.0
+ actions:
+ - name: set
+ flag: invalid_elevation
+ ignore: rejected observations
+ - name: reject
+ - filter: Domain Check # land only, no sea ice
+ where:
+ - variable:
+ name: GeoVaLs/fraction_of_ice
+ maxvalue: 0.0
+ actions:
+ - name: set
+ flag: seaice_check
+ ignore: rejected observations
+ - name: reject
+ - filter: RejectList # no land-ice
+ where:
+ - variable:
+ name: GeoVaLs/vtype
+ minvalue: 14.5
+ maxvalue: 15.5
+ actions:
+ - name: set
+ flag: landice_check
+ ignore: rejected observations
+ - name: reject
+ - filter: Difference Check # elevation check
+ reference: MetaData/stationElevation
+ value: GeoVaLs/filtered_orography
+ threshold: 800.
+ actions:
+ - name: set
+ flag: elevation_bkgdiff
+ ignore: rejected observations
+ - name: reject
+ # Add inflate error characterized by a function of elevation difference
+ - filter: Variable Assignment
+ assignments:
+ - name: DerivedMetaData/elevation_diff
+ type: float
+ function:
+ name: ObsFunction/Arithmetic
+ options:
+ variables: [MetaData/stationElevation, GeoVaLs/filtered_orography]
+ coefficients: [1., -1.]
+ total exponent: 2
+ total coefficient: 0.0000015625 #1/(800*800)
+ - filter: Variable Assignment
+ assignments:
+ - name: DerivedMetaData/elevation_diff_exp
+ type: float
+ function:
+ name: ObsFunction/Exponential
+ options:
+ variables: [DerivedMetaData/elevation_diff]
+ coeffA: 1.
+ coeffB: -1.
+ coeffC: 0.
+ coeffD: 1.
+ - filter: Variable Assignment
+ assignments:
+ - name: DerivedMetaData/elevation_diff_exp_inv
+ type: float
+ function:
+ name: ObsFunction/Arithmetic
+ options:
+ variables: [DerivedMetaData/elevation_diff_exp]
+ total exponent: -1.
+ - filter: Perform Action
+ filter variables:
+ - name: totalSnowDepth
+ where:
+ - variable:
+ name: ObsValue/totalSnowDepth
+ minvalue: 0.
+ action:
+ name: inflate error
+ inflation variable: DerivedMetaData/elevation_diff_exp_inv # 2.0
+ - filter: BlackList
+ where:
+ - variable:
+ name: MetaData/stationIdentification
+ is_in: {{ get_conventional_rejected_stations(observation_from_jcb) }}
+ actions:
+ - name: set
+ flag: rejectlist
+ ignore: rejected observations
+ - name: reject
+ obs post filters:
+ - filter: Background Check # gross error check
+ filter variables:
+ - name: totalSnowDepth
+ absolute threshold: 250
+ bias correction parameter: 1.0
+ actions:
+ - name: set
+ flag: background_check
+ ignore: rejected observations
+ - name: reject
+
diff --git a/parm/jcb-gdas/observations/snow/sfcsno.yaml.j2 b/parm/jcb-gdas/observations/snow/sfcsno.yaml.j2
new file mode 100644
index 000000000..a465cbe3e
--- /dev/null
+++ b/parm/jcb-gdas/observations/snow/sfcsno.yaml.j2
@@ -0,0 +1,217 @@
+-
+
+ # Observation Space (I/O)
+ # -----------------------
+ obs space:
+ name: {{observation_from_jcb}}
+ obsdatain:
+ engine:
+ type: bufr
+ obsfile: "{{snow_obsdatain_path}}/{{snow_obsdatain_prefix}}{{observation_from_jcb}}{{snow_obsdatain_suffix}}"
+ mapping file: "{{snow_obsdatain_path}}/bufr_sfcsno_mapping.yaml"
+ missing file action: warn
+ obsgrouping:
+ group variables: [stationIdentification]
+ obsdataout:
+ engine:
+ type: H5File
+ obsfile: "{{snow_obsdataout_path}}/{{snow_obsdataout_prefix}}{{observation_from_jcb}}{{snow_obsdataout_suffix}}"
+ simulated variables: [totalSnowDepth]
+ #
+
+ # Observation Operator
+ # --------------------
+ obs operator:
+ name: Identity
+ #
+
+ # Observation Filters (QC)
+ # ------------------------
+ obs pre filters:
+ - filter: Create Diagnostic Flags
+ flags:
+ - name: missing_snowdepth
+ initial value: false
+ - name: missing_elevation
+ initial value: false
+ - name: temporal_thinning
+ initial value: false
+ - name: invalid_snowdepth
+ initial value: false
+ - name: invalid_elevation
+ initial value: false
+ - name: land_check
+ initial value: false
+ - name: landice_check
+ initial value: false
+ - name: seaice_check
+ initial value: false
+ - name: elevation_bkgdiff
+ initial value: false
+ - name: rejectlist
+ initial value: false
+ - name: background_check
+ initial value: false
+ - filter: Perform Action
+ filter variables:
+ - name: totalSnowDepth
+ action:
+ name: assign error
+ error parameter: 40.0
+ - filter: Domain Check
+ where:
+ - variable:
+ name: ObsValue/totalSnowDepth
+ value: is_valid
+ actions:
+ - name: set
+ flag: missing_snowdepth
+ ignore: rejected observations
+ - name: reject
+ - filter: Domain Check
+ where:
+ - variable:
+ name: MetaData/stationElevation
+ value: is_valid
+ actions:
+ - name: set
+ flag: missing_elevation
+ ignore: rejected observations
+ - name: reject
+ - filter: Temporal Thinning
+ min_spacing: '{{ window_length }}'
+ seed_time: '{{ snow_background_time_iso }}'
+ category_variable:
+ name: MetaData/stationIdentification
+ actions:
+ - name: set
+ flag: temporal_thinning
+ ignore: rejected observations
+ - name: reject
+ obs prior filters:
+ - filter: Bounds Check
+ filter variables:
+ - name: totalSnowDepth
+ minvalue: 0.0
+ maxvalue: 20000.0
+ actions:
+ - name: set
+ flag: invalid_snowdepth
+ ignore: rejected observations
+ - name: reject
+ - filter: Domain Check # land only
+ where:
+ - variable:
+ name: GeoVaLs/fraction_of_land
+ minvalue: 0.5
+ actions:
+ - name: set
+ flag: land_check
+ ignore: rejected observations
+ - name: reject
+ - filter: Domain Check
+ where:
+ - variable:
+ name: MetaData/stationElevation
+ minvalue: -200.0
+ maxvalue: 3000.0
+ actions:
+ - name: set
+ flag: invalid_elevation
+ ignore: rejected observations
+ - name: reject
+ - filter: Domain Check # land only, no sea ice
+ where:
+ - variable:
+ name: GeoVaLs/fraction_of_ice
+ maxvalue: 0.0
+ actions:
+ - name: set
+ flag: seaice_check
+ ignore: rejected observations
+ - name: reject
+ - filter: RejectList # no land-ice
+ where:
+ - variable:
+ name: GeoVaLs/vtype
+ minvalue: 14.5
+ maxvalue: 15.5
+ actions:
+ - name: set
+ flag: landice_check
+ ignore: rejected observations
+ - name: reject
+ - filter: Difference Check # elevation check
+ reference: MetaData/stationElevation
+ value: GeoVaLs/filtered_orography
+ threshold: 800.
+ actions:
+ - name: set
+ flag: elevation_bkgdiff
+ ignore: rejected observations
+ - name: reject
+ # Add inflate error characterized by a function of elevation difference
+ - filter: Variable Assignment
+ assignments:
+ - name: DerivedMetaData/elevation_diff
+ type: float
+ function:
+ name: ObsFunction/Arithmetic
+ options:
+ variables: [MetaData/stationElevation, GeoVaLs/filtered_orography]
+ coefficients: [1., -1.]
+ total exponent: 2
+ total coefficient: 0.0000015625 #1/(800*800)
+ - filter: Variable Assignment
+ assignments:
+ - name: DerivedMetaData/elevation_diff_exp
+ type: float
+ function:
+ name: ObsFunction/Exponential
+ options:
+ variables: [DerivedMetaData/elevation_diff]
+ coeffA: 1.
+ coeffB: -1.
+ coeffC: 0.
+ coeffD: 1.
+ - filter: Variable Assignment
+ assignments:
+ - name: DerivedMetaData/elevation_diff_exp_inv
+ type: float
+ function:
+ name: ObsFunction/Arithmetic
+ options:
+ variables: [DerivedMetaData/elevation_diff_exp]
+ total exponent: -1.
+ - filter: Perform Action
+ filter variables:
+ - name: totalSnowDepth
+ where:
+ - variable:
+ name: ObsValue/totalSnowDepth
+ minvalue: 0.
+ action:
+ name: inflate error
+ inflation variable: DerivedMetaData/elevation_diff_exp_inv # 2.0
+ - filter: BlackList
+ where:
+ - variable:
+ name: MetaData/stationIdentification
+ is_in: {{ get_conventional_rejected_stations(observation_from_jcb) }}
+ actions:
+ - name: set
+ flag: rejectlist
+ ignore: rejected observations
+ - name: reject
+ obs post filters:
+ - filter: Background Check # gross error check
+ filter variables:
+ - name: totalSnowDepth
+ absolute threshold: 250
+ bias correction parameter: 1.0
+ actions:
+ - name: set
+ flag: background_check
+ ignore: rejected observations
+ - name: reject
+
diff --git a/parm/jcb-gdas/observations/snow/snocvr.yaml.j2 b/parm/jcb-gdas/observations/snow/snocvr.yaml.j2
new file mode 100644
index 000000000..0626a145b
--- /dev/null
+++ b/parm/jcb-gdas/observations/snow/snocvr.yaml.j2
@@ -0,0 +1,217 @@
+-
+
+ # Observation Space (I/O)
+ # -----------------------
+ obs space:
+ name: {{observation_from_jcb}}
+ obsdatain:
+ engine:
+ type: bufr
+ obsfile: "{{snow_obsdatain_path}}/{{snow_obsdatain_prefix}}{{observation_from_jcb}}{{snow_obsdatain_suffix}}"
+ mapping file: "{{snow_obsdatain_path}}/bufr_snocvr_mapping.yaml"
+ missing file action: warn
+ obsgrouping:
+ group variables: [stationIdentification]
+ obsdataout:
+ engine:
+ type: H5File
+ obsfile: "{{snow_obsdataout_path}}/{{snow_obsdataout_prefix}}{{observation_from_jcb}}{{snow_obsdataout_suffix}}"
+ simulated variables: [totalSnowDepth]
+ #
+
+ # Observation Operator
+ # --------------------
+ obs operator:
+ name: Identity
+ #
+
+ # Observation Filters (QC)
+ # ------------------------
+ obs pre filters:
+ - filter: Create Diagnostic Flags
+ flags:
+ - name: missing_snowdepth
+ initial value: false
+ - name: missing_elevation
+ initial value: false
+ - name: temporal_thinning
+ initial value: false
+ - name: invalid_snowdepth
+ initial value: false
+ - name: invalid_elevation
+ initial value: false
+ - name: land_check
+ initial value: false
+ - name: landice_check
+ initial value: false
+ - name: seaice_check
+ initial value: false
+ - name: elevation_bkgdiff
+ initial value: false
+ - name: rejectlist
+ initial value: false
+ - name: background_check
+ initial value: false
+ - filter: Perform Action
+ filter variables:
+ - name: totalSnowDepth
+ action:
+ name: assign error
+ error parameter: 40.0
+ - filter: Domain Check
+ where:
+ - variable:
+ name: ObsValue/totalSnowDepth
+ value: is_valid
+ actions:
+ - name: set
+ flag: missing_snowdepth
+ ignore: rejected observations
+ - name: reject
+ - filter: Domain Check
+ where:
+ - variable:
+ name: MetaData/stationElevation
+ value: is_valid
+ actions:
+ - name: set
+ flag: missing_elevation
+ ignore: rejected observations
+ - name: reject
+ - filter: Temporal Thinning
+ min_spacing: '{{ window_length }}'
+ seed_time: '{{ snow_background_time_iso }}'
+ category_variable:
+ name: MetaData/stationIdentification
+ actions:
+ - name: set
+ flag: temporal_thinning
+ ignore: rejected observations
+ - name: reject
+ obs prior filters:
+ - filter: Bounds Check
+ filter variables:
+ - name: totalSnowDepth
+ minvalue: 0.0
+ maxvalue: 20000.0
+ actions:
+ - name: set
+ flag: invalid_snowdepth
+ ignore: rejected observations
+ - name: reject
+ - filter: Domain Check # land only
+ where:
+ - variable:
+ name: GeoVaLs/fraction_of_land
+ minvalue: 0.5
+ actions:
+ - name: set
+ flag: land_check
+ ignore: rejected observations
+ - name: reject
+ - filter: Domain Check
+ where:
+ - variable:
+ name: MetaData/stationElevation
+ minvalue: -200.0
+ maxvalue: 3000.0
+ actions:
+ - name: set
+ flag: invalid_elevation
+ ignore: rejected observations
+ - name: reject
+ - filter: Domain Check # land only, no sea ice
+ where:
+ - variable:
+ name: GeoVaLs/fraction_of_ice
+ maxvalue: 0.0
+ actions:
+ - name: set
+ flag: seaice_check
+ ignore: rejected observations
+ - name: reject
+ - filter: RejectList # no land-ice
+ where:
+ - variable:
+ name: GeoVaLs/vtype
+ minvalue: 14.5
+ maxvalue: 15.5
+ actions:
+ - name: set
+ flag: landice_check
+ ignore: rejected observations
+ - name: reject
+ - filter: Difference Check # elevation check
+ reference: MetaData/stationElevation
+ value: GeoVaLs/filtered_orography
+ threshold: 800.
+ actions:
+ - name: set
+ flag: elevation_bkgdiff
+ ignore: rejected observations
+ - name: reject
+ # Add inflate error characterized by a function of elevation difference
+ - filter: Variable Assignment
+ assignments:
+ - name: DerivedMetaData/elevation_diff
+ type: float
+ function:
+ name: ObsFunction/Arithmetic
+ options:
+ variables: [MetaData/stationElevation, GeoVaLs/filtered_orography]
+ coefficients: [1., -1.]
+ total exponent: 2
+ total coefficient: 0.0000015625 #1/(800*800)
+ - filter: Variable Assignment
+ assignments:
+ - name: DerivedMetaData/elevation_diff_exp
+ type: float
+ function:
+ name: ObsFunction/Exponential
+ options:
+ variables: [DerivedMetaData/elevation_diff]
+ coeffA: 1.
+ coeffB: -1.
+ coeffC: 0.
+ coeffD: 1.
+ - filter: Variable Assignment
+ assignments:
+ - name: DerivedMetaData/elevation_diff_exp_inv
+ type: float
+ function:
+ name: ObsFunction/Arithmetic
+ options:
+ variables: [DerivedMetaData/elevation_diff_exp]
+ total exponent: -1.
+ - filter: Perform Action
+ filter variables:
+ - name: totalSnowDepth
+ where:
+ - variable:
+ name: ObsValue/totalSnowDepth
+ minvalue: 0.
+ action:
+ name: inflate error
+ inflation variable: DerivedMetaData/elevation_diff_exp_inv # 2.0
+ - filter: BlackList
+ where:
+ - variable:
+ name: MetaData/stationIdentification
+ is_in: {{ get_conventional_rejected_stations(observation_from_jcb) }}
+ actions:
+ - name: set
+ flag: rejectlist
+ ignore: rejected observations
+ - name: reject
+ obs post filters:
+ - filter: Background Check # gross error check
+ filter variables:
+ - name: totalSnowDepth
+ absolute threshold: 250
+ bias correction parameter: 1.0
+ actions:
+ - name: set
+ flag: background_check
+ ignore: rejected observations
+ - name: reject
+
diff --git a/parm/jcb-gdas/observations/snow/snocvr_snomad.yaml.j2 b/parm/jcb-gdas/observations/snow/snocvr_snomad.yaml.j2
new file mode 100644
index 000000000..9d9d64825
--- /dev/null
+++ b/parm/jcb-gdas/observations/snow/snocvr_snomad.yaml.j2
@@ -0,0 +1,216 @@
+-
+
+ # Observation Space (I/O)
+ # -----------------------
+ obs space:
+ name: {{observation_from_jcb}}
+ obsdatain:
+ engine:
+ type: H5File
+ obsfile: "{{snow_prepobs_path}}/{{snow_obsdatain_prefix}}{{observation_from_jcb}}.tm00.nc"
+ missing file action: warn
+ obsgrouping:
+ group variables: [stationIdentification]
+ obsdataout:
+ engine:
+ type: H5File
+ obsfile: "{{snow_obsdataout_path}}/{{snow_obsdataout_prefix}}{{observation_from_jcb}}{{snow_obsdataout_suffix}}"
+ simulated variables: [totalSnowDepth]
+ #
+
+ # Observation Operator
+ # --------------------
+ obs operator:
+ name: Identity
+ #
+
+ # Observation Filters (QC)
+ # ------------------------
+ obs pre filters:
+ - filter: Create Diagnostic Flags
+ flags:
+ - name: missing_snowdepth
+ initial value: false
+ - name: missing_elevation
+ initial value: false
+ - name: temporal_thinning
+ initial value: false
+ - name: invalid_snowdepth
+ initial value: false
+ - name: invalid_elevation
+ initial value: false
+ - name: land_check
+ initial value: false
+ - name: landice_check
+ initial value: false
+ - name: seaice_check
+ initial value: false
+ - name: elevation_bkgdiff
+ initial value: false
+ - name: rejectlist
+ initial value: false
+ - name: background_check
+ initial value: false
+ - filter: Perform Action
+ filter variables:
+ - name: totalSnowDepth
+ action:
+ name: assign error
+ error parameter: 40.0
+ - filter: Domain Check
+ where:
+ - variable:
+ name: ObsValue/totalSnowDepth
+ value: is_valid
+ actions:
+ - name: set
+ flag: missing_snowdepth
+ ignore: rejected observations
+ - name: reject
+ - filter: Domain Check
+ where:
+ - variable:
+ name: MetaData/stationElevation
+ value: is_valid
+ actions:
+ - name: set
+ flag: missing_elevation
+ ignore: rejected observations
+ - name: reject
+ - filter: Temporal Thinning
+ min_spacing: '{{ window_length }}'
+ seed_time: '{{ snow_background_time_iso }}'
+ category_variable:
+ name: MetaData/stationIdentification
+ actions:
+ - name: set
+ flag: temporal_thinning
+ ignore: rejected observations
+ - name: reject
+ obs prior filters:
+ - filter: Bounds Check
+ filter variables:
+ - name: totalSnowDepth
+ minvalue: 0.0
+ maxvalue: 20000.0
+ actions:
+ - name: set
+ flag: invalid_snowdepth
+ ignore: rejected observations
+ - name: reject
+ - filter: Domain Check # land only
+ where:
+ - variable:
+ name: GeoVaLs/fraction_of_land
+ minvalue: 0.5
+ actions:
+ - name: set
+ flag: land_check
+ ignore: rejected observations
+ - name: reject
+ - filter: Domain Check
+ where:
+ - variable:
+ name: MetaData/stationElevation
+ minvalue: -200.0
+ maxvalue: 3000.0
+ actions:
+ - name: set
+ flag: invalid_elevation
+ ignore: rejected observations
+ - name: reject
+ - filter: Domain Check # land only, no sea ice
+ where:
+ - variable:
+ name: GeoVaLs/fraction_of_ice
+ maxvalue: 0.0
+ actions:
+ - name: set
+ flag: seaice_check
+ ignore: rejected observations
+ - name: reject
+ - filter: RejectList # no land-ice
+ where:
+ - variable:
+ name: GeoVaLs/vtype
+ minvalue: 14.5
+ maxvalue: 15.5
+ actions:
+ - name: set
+ flag: landice_check
+ ignore: rejected observations
+ - name: reject
+ - filter: Difference Check # elevation check
+ reference: MetaData/stationElevation
+ value: GeoVaLs/filtered_orography
+ threshold: 800.
+ actions:
+ - name: set
+ flag: elevation_bkgdiff
+ ignore: rejected observations
+ - name: reject
+ # Add inflate error characterized by a function of elevation difference
+ - filter: Variable Assignment
+ assignments:
+ - name: DerivedMetaData/elevation_diff
+ type: float
+ function:
+ name: ObsFunction/Arithmetic
+ options:
+ variables: [MetaData/stationElevation, GeoVaLs/filtered_orography]
+ coefficients: [1., -1.]
+ total exponent: 2
+ total coefficient: 0.0000015625 #1/(800*800)
+ - filter: Variable Assignment
+ assignments:
+ - name: DerivedMetaData/elevation_diff_exp
+ type: float
+ function:
+ name: ObsFunction/Exponential
+ options:
+ variables: [DerivedMetaData/elevation_diff]
+ coeffA: 1.
+ coeffB: -1.
+ coeffC: 0.
+ coeffD: 1.
+ - filter: Variable Assignment
+ assignments:
+ - name: DerivedMetaData/elevation_diff_exp_inv
+ type: float
+ function:
+ name: ObsFunction/Arithmetic
+ options:
+ variables: [DerivedMetaData/elevation_diff_exp]
+ total exponent: -1.
+ - filter: Perform Action
+ filter variables:
+ - name: totalSnowDepth
+ where:
+ - variable:
+ name: ObsValue/totalSnowDepth
+ minvalue: 0.
+ action:
+ name: inflate error
+ inflation variable: DerivedMetaData/elevation_diff_exp_inv # 2.0
+ - filter: BlackList
+ where:
+ - variable:
+ name: MetaData/stationIdentification
+ is_in: {{ get_conventional_rejected_stations(observation_from_jcb) }}
+ actions:
+ - name: set
+ flag: rejectlist
+ ignore: rejected observations
+ - name: reject
+ obs post filters:
+ - filter: Background Check # gross error check
+ filter variables:
+ - name: totalSnowDepth
+ absolute threshold: 250
+ bias correction parameter: 1.0
+ actions:
+ - name: set
+ flag: background_check
+ ignore: rejected observations
+ - name: reject
+
diff --git a/parm/jcb-gdas/observations/snow/snomad.yaml.j2 b/parm/jcb-gdas/observations/snow/snomad.yaml.j2
new file mode 100644
index 000000000..58a23ac10
--- /dev/null
+++ b/parm/jcb-gdas/observations/snow/snomad.yaml.j2
@@ -0,0 +1,217 @@
+-
+
+ # Observation Space (I/O)
+ # -----------------------
+ obs space:
+ name: {{observation_from_jcb}}
+ obsdatain:
+ engine:
+ type: bufr
+ obsfile: "{{snow_obsdatain_path}}/{{snow_obsdatain_prefix}}{{observation_from_jcb}}{{snow_obsdatain_suffix}}"
+ mapping file: "{{snow_obsdatain_path}}/bufr_snomad_mapping.yaml"
+ missing file action: warn
+ obsgrouping:
+ group variables: [stationIdentification]
+ obsdataout:
+ engine:
+ type: H5File
+ obsfile: "{{snow_obsdataout_path}}/{{snow_obsdataout_prefix}}{{observation_from_jcb}}{{snow_obsdataout_suffix}}"
+ simulated variables: [totalSnowDepth]
+ #
+
+ # Observation Operator
+ # --------------------
+ obs operator:
+ name: Identity
+ #
+
+ # Observation Filters (QC)
+ # ------------------------
+ obs pre filters:
+ - filter: Create Diagnostic Flags
+ flags:
+ - name: missing_snowdepth
+ initial value: false
+ - name: missing_elevation
+ initial value: false
+ - name: temporal_thinning
+ initial value: false
+ - name: invalid_snowdepth
+ initial value: false
+ - name: invalid_elevation
+ initial value: false
+ - name: land_check
+ initial value: false
+ - name: landice_check
+ initial value: false
+ - name: seaice_check
+ initial value: false
+ - name: elevation_bkgdiff
+ initial value: false
+ - name: rejectlist
+ initial value: false
+ - name: background_check
+ initial value: false
+ - filter: Perform Action
+ filter variables:
+ - name: totalSnowDepth
+ action:
+ name: assign error
+ error parameter: 40.0
+ - filter: Domain Check
+ where:
+ - variable:
+ name: ObsValue/totalSnowDepth
+ value: is_valid
+ actions:
+ - name: set
+ flag: missing_snowdepth
+ ignore: rejected observations
+ - name: reject
+ - filter: Domain Check
+ where:
+ - variable:
+ name: MetaData/stationElevation
+ value: is_valid
+ actions:
+ - name: set
+ flag: missing_elevation
+ ignore: rejected observations
+ - name: reject
+ - filter: Temporal Thinning
+ min_spacing: '{{ window_length }}'
+ seed_time: '{{ snow_background_time_iso }}'
+ category_variable:
+ name: MetaData/stationIdentification
+ actions:
+ - name: set
+ flag: temporal_thinning
+ ignore: rejected observations
+ - name: reject
+ obs prior filters:
+ - filter: Bounds Check
+ filter variables:
+ - name: totalSnowDepth
+ minvalue: 0.0
+ maxvalue: 20000.0
+ actions:
+ - name: set
+ flag: invalid_snowdepth
+ ignore: rejected observations
+ - name: reject
+ - filter: Domain Check # land only
+ where:
+ - variable:
+ name: GeoVaLs/fraction_of_land
+ minvalue: 0.5
+ actions:
+ - name: set
+ flag: land_check
+ ignore: rejected observations
+ - name: reject
+ - filter: Domain Check
+ where:
+ - variable:
+ name: MetaData/stationElevation
+ minvalue: -200.0
+ maxvalue: 3000.0
+ actions:
+ - name: set
+ flag: invalid_elevation
+ ignore: rejected observations
+ - name: reject
+ - filter: Domain Check # land only, no sea ice
+ where:
+ - variable:
+ name: GeoVaLs/fraction_of_ice
+ maxvalue: 0.0
+ actions:
+ - name: set
+ flag: seaice_check
+ ignore: rejected observations
+ - name: reject
+ - filter: RejectList # no land-ice
+ where:
+ - variable:
+ name: GeoVaLs/vtype
+ minvalue: 14.5
+ maxvalue: 15.5
+ actions:
+ - name: set
+ flag: landice_check
+ ignore: rejected observations
+ - name: reject
+ - filter: Difference Check # elevation check
+ reference: MetaData/stationElevation
+ value: GeoVaLs/filtered_orography
+ threshold: 800.
+ actions:
+ - name: set
+ flag: elevation_bkgdiff
+ ignore: rejected observations
+ - name: reject
+ # Add inflate error characterized by a function of elevation difference
+ - filter: Variable Assignment
+ assignments:
+ - name: DerivedMetaData/elevation_diff
+ type: float
+ function:
+ name: ObsFunction/Arithmetic
+ options:
+ variables: [MetaData/stationElevation, GeoVaLs/filtered_orography]
+ coefficients: [1., -1.]
+ total exponent: 2
+ total coefficient: 0.0000015625 #1/(800*800)
+ - filter: Variable Assignment
+ assignments:
+ - name: DerivedMetaData/elevation_diff_exp
+ type: float
+ function:
+ name: ObsFunction/Exponential
+ options:
+ variables: [DerivedMetaData/elevation_diff]
+ coeffA: 1.
+ coeffB: -1.
+ coeffC: 0.
+ coeffD: 1.
+ - filter: Variable Assignment
+ assignments:
+ - name: DerivedMetaData/elevation_diff_exp_inv
+ type: float
+ function:
+ name: ObsFunction/Arithmetic
+ options:
+ variables: [DerivedMetaData/elevation_diff_exp]
+ total exponent: -1.
+ - filter: Perform Action
+ filter variables:
+ - name: totalSnowDepth
+ where:
+ - variable:
+ name: ObsValue/totalSnowDepth
+ minvalue: 0.
+ action:
+ name: inflate error
+ inflation variable: DerivedMetaData/elevation_diff_exp_inv # 2.0
+ - filter: BlackList
+ where:
+ - variable:
+ name: MetaData/stationIdentification
+ is_in: {{ get_conventional_rejected_stations(observation_from_jcb) }}
+ actions:
+ - name: set
+ flag: rejectlist
+ ignore: rejected observations
+ - name: reject
+ obs post filters:
+ - filter: Background Check # gross error check
+ filter variables:
+ - name: totalSnowDepth
+ absolute threshold: 250
+ bias correction parameter: 1.0
+ actions:
+ - name: set
+ flag: background_check
+ ignore: rejected observations
+ - name: reject
+
diff --git a/parm/jcb-gdas/observations/soil/smap_soil.yaml.j2 b/parm/jcb-gdas/observations/soil/smap_soil.yaml.j2
new file mode 100644
index 000000000..760e5344e
--- /dev/null
+++ b/parm/jcb-gdas/observations/soil/smap_soil.yaml.j2
@@ -0,0 +1,196 @@
+-
+
+ # Observation Space (I/O)
+ # -----------------------
+ obs space:
+ name: {{observation_from_jcb}}
+ obsdatain:
+ engine:
+ type: H5File
+ obsfile: "{{soil_obsdatain_path}}/{{soil_obsdatain_prefix}}{{observation_from_jcb}}.nc"
+ missing file action: warn
+ obsdataout:
+ engine:
+ type: H5File
+ obsfile: "{{soil_obsdataout_path}}/{{soil_obsdataout_prefix}}{{observation_from_jcb}}{{soil_obsdataout_suffix}}"
+ simulated variables: [soilMoistureVolumetric]
+ #
+
+ # Observation Operator
+ # --------------------
+ obs operator:
+ name: Identity
+ #
+
+ # Observation Filters (QC)
+ # ------------------------
+ obs pre filters:
+ - filter: Create Diagnostic Flags
+ flags:
+ - name: missing_smc
+ initial value: false
+# - name: missing_elevation
+# initial value: false
+ - name: invalid_smc
+ initial value: false
+# - name: invalid_elevation
+# initial value: false
+ - name: land_check
+ initial value: false
+ - name: landice_check
+ initial value: false
+ - name: seaice_check
+ initial value: false
+ - name: snow_check
+ initial value: false
+ - name: retrv_qual_check
+ initial value: false
+ - name: vegtype_check
+ initial value: false
+ - name: elevation_bkgdiff
+ initial value: false
+# - name: rejectlist
+# initial value: false
+ - name: background_check
+ initial value: false
+ - filter: Perform Action
+ filter variables:
+ - name: soilMoistureVolumetric
+ action:
+ name: assign error
+ error parameter: 0.20
+ - filter: Domain Check
+ where:
+ - variable:
+ name: ObsValue/soilMoistureVolumetric
+ value: is_valid
+ actions:
+ - name: set
+ flag: missing_smc
+ ignore: rejected observations
+ - name: reject
+# - filter: Domain Check
+# where:
+# - variable:
+# name: MetaData/stationElevation
+# value: is_valid
+# actions:
+# - name: set
+# flag: missing_elevation
+# ignore: rejected observations
+# - name: reject
+ obs prior filters:
+ - filter: Bounds Check
+ filter variables:
+ - name: soilMoistureVolumetric
+ minvalue: 0.0
+ maxvalue: 1.0
+ actions:
+ - name: set
+ flag: invalid_smc
+ ignore: rejected observations
+ - name: reject
+ - filter: Domain Check # land only
+ where:
+ - variable:
+ name: GeoVaLs/fraction_of_land
+ minvalue: 0.5
+ actions:
+ - name: set
+ flag: land_check
+ ignore: rejected observations
+ - name: reject
+# - filter: Domain Check
+# where:
+# - variable:
+# name: MetaData/stationElevation
+# minvalue: -200.0
+# maxvalue: 9000.0
+# actions:
+# - name: set
+# flag: invalid_elevation
+# ignore: rejected observations
+# - name: reject
+ - filter: Domain Check # land only, no sea ice
+ where:
+ - variable:
+ name: GeoVaLs/fraction_of_ice
+ maxvalue: 0.0
+ actions:
+ - name: set
+ flag: seaice_check
+ ignore: rejected observations
+ - name: reject
+ - filter: Domain Check # no snow
+ where:
+ - variable:
+ name: GeoVaLs/sheleg
+ maxvalue: 0.0
+ actions:
+ - name: set
+ flag: snow_check
+ ignore: rejected observations
+ - name: reject
+ - filter: Domain Check # high-quality retrievals
+ where:
+ - variable:
+ name: PreQC/soilMoistureVolumetric
+ is_in: 0, 8
+ actions:
+ - name: set
+ flag: retrv_qual_check
+ ignore: rejected observations
+ - name: reject
+ - filter: RejectList # no land-ice
+ where:
+ - variable:
+ name: GeoVaLs/vtype
+ minvalue: 14.5
+ maxvalue: 15.5
+ actions:
+ - name: set
+ flag: landice_check
+ ignore: rejected observations
+ - name: reject
+ - filter: RejectList # exclude certain IGBP vegetation types
+ where:
+ - variable:
+ name: GeoVaLs/vtype
+ absolute_tolerance: 1.0e-3
+ is_close_to_any_of: [1, 2, 3, 4, 13, 15, 17]
+ actions:
+ - name: set
+ flag: vegtype_check
+ ignore: rejected observations
+ - name: reject
+# - filter: Difference Check # elevation check
+# reference: MetaData/stationElevation
+# value: GeoVaLs/filtered_orography
+# threshold: 800.
+# actions:
+# - name: set
+# flag: elevation_bkgdiff
+# ignore: rejected observations
+# - name: reject
+# - filter: BlackList
+# where:
+# - variable:
+# name: MetaData/stationIdentification
+# is_in: {{ get_conventional_rejected_stations(observation_from_jcb) }}
+# actions:
+# - name: set
+# flag: rejectlist
+# ignore: rejected observations
+# - name: reject
+ obs post filters:
+ - filter: Background Check # gross error check
+ filter variables:
+ - name: soilMoistureVolumetric
+ #threshold: 5
+ absolute threshold: 0.5
+ bias correction parameter: 1.0
+ actions:
+ - name: set
+ flag: background_check
+ ignore: rejected observations
+ - name: reject
diff --git a/parm/jcb-gdas/test/client_integration/gdas-atmosphere-templates.yaml b/parm/jcb-gdas/test/client_integration/gdas-atmosphere-templates.yaml
new file mode 100644
index 000000000..4e57bd759
--- /dev/null
+++ b/parm/jcb-gdas/test/client_integration/gdas-atmosphere-templates.yaml
@@ -0,0 +1,165 @@
+# This part is for testing only. Normally this would just show algorithm:
+# -----------------------------------------------------------------------------------
+supported_algorithms:
+- 3dvar
+- hofx3d
+- hofx4d
+- local_ensemble_da
+# Local algorithms
+- fv3jedi_fv3inc_lgetkf
+- fv3jedi_fv3inc_variational
+
+# This is overwritten in the testing but allows command line test of jcb
+algorithm: fv3jedi_fv3inc_lgetkf
+
+# Search path for model and obs for JCB (relative for the submodule, or can be absolute)
+# --------------------------------------------------------------------------------------
+app_path_algorithm: gdas/algorithm/atmosphere
+app_path_model: gdas/model/atmosphere
+app_path_observations: gdas/observations/atmosphere
+app_path_observation_chronicle: gdas/observation_chronicle/atmosphere
+
+
+# Places where we deviate from the generic file name of a yaml
+# ------------------------------------------------------------
+final_increment_file: atmosphere_final_increment_gaussian
+output_ensemble_increments_file: atmosphere_output_ensemble_increments_gaussian
+model_file: atmosphere_model_pseudo
+initial_condition_file: atmosphere_background
+background_error_file: atmosphere_background_error_hybrid_gsibec_bump
+
+
+# Global analysis things
+# ----------------------
+window_begin: '2024-02-01T00:00:00Z'
+window_length: PT6H
+bound_to_include: begin
+minimizer: DRPCG
+final_diagnostics_departures: anlmob
+analysis_variables: [eastward_wind,northward_wind,air_temperature,air_pressure_at_surface,water_vapor_mixing_ratio_wrt_moist_air,ice_wat,liq_wat,o3mr]
+number_of_outer_loops: 2
+
+# Testing
+# -------
+
+do_testing: false
+
+# Model things
+# ------------
+atmosphere_layout_x: 2
+atmosphere_layout_y: 2
+atmosphere_npx_ges: 361
+atmosphere_npy_ges: 361
+atmosphere_npz_ges: 127
+atmosphere_npx_his: 361
+atmosphere_npy_his: 361
+atmosphere_npz_his: 127
+atmosphere_npx_anl: 361
+atmosphere_npy_anl: 361
+atmosphere_npz_anl: 127
+atmosphere_fv3jedi_files_path: DATA/fv3jedi
+
+# Background
+atmosphere_background_path: DATA/bkg
+atmosphere_background_ensemble_path: "DATA/ens/mem%mem%"
+
+atmosphere_variational_history_prefix: "bkg_"
+atmosphere_ensemble_history_prefix: "ens_"
+
+atmosphere_variational_analysis_prefix: "anl_"
+atmosphere_ensemble_analysis_prefix: "anl_"
+
+atmosphere_background_time_iso: '2024-02-02T00:00:00Z'
+
+# Background error
+atmosphere_bump_data_directory: DATA/berror
+atmosphere_gsibec_path: DATA/berror
+atmosphere_number_ensemble_members: 3
+atmosphere_layout_gsib_x: 2
+atmosphere_layout_gsib_y: 2
+
+# Minimization options
+atmosphere_ninner_1: 4
+atmosphere_ninner_2: 2
+atmosphere_grad_red_1: 1e-5
+atmosphere_grad_red_2: 1e-5
+
+# Forecasting
+atmosphere_forecast_length: PT6H
+atmosphere_forecast_timestep: PT1H
+
+# Write final increment on Gaussian grid in variational
+atmosphere_variational_increment_type: "gaussian"
+atmosphere_final_increment_prefix: "./anl/atminc."
+
+# Observation things
+# ------------------
+observations: all_observations
+
+# JCB level option to replace obs filters
+# ---------------------------------------
+replace_obs_filters:
+ observations:
+ - abi_g16
+ override_filters:
+ - filter: PreQC
+ maxvalue: 1.0
+ action:
+ name: reject
+
+crtm_coefficient_path: "DATA/crtm/"
+
+# Naming conventions for observational files
+atmosphere_obsdatain_path: DATA/obs
+atmosphere_obsdatain_prefix: OPREFIX
+atmosphere_obsdatain_suffix: ".2024020100.nc"
+
+atmosphere_obsdataout_path: DATA/diags
+atmosphere_obsdataout_prefix: diag
+atmosphere_obsdataout_suffix: "_2024020100.nc"
+
+# Naming conventions for bias correction files
+atmosphere_obsbiasin_path: DATA/obs
+atmosphere_obsbiasin_prefix: GPREFIX
+atmosphere_obsbiasin_suffix: ".satbias.nc"
+atmosphere_obsbiasin_acft_suffix: ".acft_out.nc"
+atmosphere_obstlapsein_prefix: GPREFIX
+atmosphere_obstlapsein_suffix: ".tlapse.txt"
+atmosphere_obsbiascovin_prefix: GPREFIX
+atmosphere_obsbiascovin_suffix: ".satbias_cov.nc"
+atmosphere_obsbiascovin_acft_suffix: ".acft_out_cov.nc"
+
+atmosphere_obsbiasout_path: DATA/bc
+atmosphere_obsbiasout_prefix: APREFIX
+atmosphere_obsbiasout_suffix: ".satbias.nc"
+atmosphere_obsbiasout_acft_suffix: ".acft_out.nc"
+atmosphere_obsbiascovout_prefix: APREFIX
+atmosphere_obsbiascovout_suffix: ".satbias_cov.nc"
+atmosphere_obsbiascovout_acft_suffix: ".acft_out_cov.nc"
+
+
+# Local Ensemble DA (LETKF)
+# -------------------------
+local_ensemble_da_solver: Deterministic GETKF
+
+increment_variables: [ua,va,DZ,delp,t,ps,sphum,ice_wat,liq_wat,o3mr]
+
+# Veritcal localization for GETKF
+vl_fraction_of_retained_variance: 0.750
+vl_lengthscale: 2.1
+vl_lengthscale_units: logp
+inflation_rtps: 0.85
+inflation_rtpp: 0.0
+inflation_mult: 1.0
+
+# Driver
+driver_update_obs_config_with_geometry_info: true
+driver_save_posterior_mean: false
+driver_save_posterior_ensemble: false
+driver_save_prior_mean: false
+driver_save_posterior_mean_increment: false
+driver_save_posterior_ensemble_increments: true
+
+# Diagnostics
+atmosphere_ensemble_increment_prefix: "./anl/mem%{member}%/atminc."
+atmosphere_posterior_output_gaussian: "./mem%{member}%/atmanl."
diff --git a/parm/jcb-gdas/test/client_integration/gdas-marine-templates.yaml b/parm/jcb-gdas/test/client_integration/gdas-marine-templates.yaml
new file mode 100644
index 000000000..b99a221bc
--- /dev/null
+++ b/parm/jcb-gdas/test/client_integration/gdas-marine-templates.yaml
@@ -0,0 +1,112 @@
+# This part is for testing only. Normally this would just show algorithm:
+# -----------------------------------------------------------------------------------
+supported_algorithms:
+- hofx3d
+- hofx4d
+- 3dfgat
+#- local_ensemble_da
+
+
+# Search path for model and obs for JCB (relative for the submodule, or can be absolute)
+# --------------------------------------------------------------------------------------
+app_path_model: gdas/model/marine
+app_path_observations: gdas/observations/marine
+app_path_observation_chronicle: gdas/observation_chronicle/marine
+
+
+# Places where we deviate from the generic file name of a yaml
+# ------------------------------------------------------------
+model_file: marine_model_pseudo
+initial_condition_file: marine_background
+background_error_file: marine_background_error_hybrid_diffusion_diffusion
+
+
+# Global analysis things
+# ----------------------
+window_begin: '2024-01-31T21:00:00Z'
+window_length: PT6H
+bound_to_include: begin
+minimizer: RPCG
+final_diagnostics_departures: oman
+analysis_variables: [cicen, hicen, hsnon, socn, tocn, uocn, vocn, ssh]
+number_of_outer_loops: 1
+
+
+# Model things
+# ------------
+marine_soca_files_path: DATA/soca
+marine_vt_levels: 25
+marine_stddev_time: '2024-01-31T21:00:00Z'
+
+# Background
+marine_background_time: '2024-01-31T21:00:00Z'
+marine_background_path: DATA/bkg
+
+
+# Background error
+marine_window_middle: '2024-02-01T00:00:00Z'
+marine_number_ensemble_members: 3
+
+# Forecasting
+marine_forecast_timestep: PT1H
+
+# Minimization
+marine_ninner_1: 3
+marine_grad_red_1: 1e-4
+
+# Forecast states
+marine_pseudo_model_states:
+- date: '2024-01-31T21:00:00Z'
+ basename: base
+ ocn_filename: ocn
+ ice_filename: ice
+ read_from_file: true
+- date: '2024-02-01T00:00:00Z'
+ basename: base
+ ocn_filename: ocn
+ ice_filename: ice
+ read_from_file: true
+- date: '2024-02-01T03:00:00Z'
+ basename: base
+ ocn_filename: ocn
+ ice_filename: ice
+ read_from_file: true
+
+# Observation things
+# ------------------
+observations: all_observations
+
+# Naming conventions for observational files
+marine_obsdatain_path: DATA/obs
+marine_obsdatain_prefix: OPREFIX
+marine_obsdatain_suffix: ".2024020100.nc"
+
+marine_obsdataout_path: DATA/diags
+marine_obsdataout_prefix: diag
+marine_obsdataout_suffix: "_2024020100.nc"
+
+# Local Ensemble DA (LETKF)
+# -------------------------
+local_ensemble_da_solver: Deterministic GETKF
+
+increment_variables: [cicen, hicen, hsnon, socn, tocn, uocn, vocn, ssh]
+
+# Veritcal localization for GETKF
+vl_fraction_of_retained_variance: 0.750
+vl_lengthscale: 2.1
+vl_lengthscale_units: logp
+inflation_rtps: 0.85
+inflation_rtpp: 0.0
+inflation_mult: 1.0
+
+# Driver
+driver_update_obs_config_with_geometry_info: true
+driver_save_posterior_mean: false
+driver_save_posterior_ensemble: false
+driver_save_prior_mean: false
+driver_save_posterior_mean_increment: false
+driver_save_posterior_ensemble_increments: true
+
+# Diagnostics
+marine_ensemble_increment_prefix: "./anl/mem%{member}%/atminc."
+marine_posterior_output_gaussian: "./mem%{member}%/atmanl."
diff --git a/sorc/fv3-jedi b/sorc/fv3-jedi
index ee024eed3..494f83c30 160000
--- a/sorc/fv3-jedi
+++ b/sorc/fv3-jedi
@@ -1 +1 @@
-Subproject commit ee024eed3b7076212eceabedad7ffc21c8a11520
+Subproject commit 494f83c308e79fd1f5549f884997bd208577643f
diff --git a/sorc/ioda b/sorc/ioda
index 0f02aadc2..cfa95b04c 160000
--- a/sorc/ioda
+++ b/sorc/ioda
@@ -1 +1 @@
-Subproject commit 0f02aadc22341fdb4dbb8e5eed13c4889e8ce487
+Subproject commit cfa95b04c0900ae0ccabe561458183ab2d6d62d0
diff --git a/sorc/oops b/sorc/oops
index 47bf8d39a..e724cafc1 160000
--- a/sorc/oops
+++ b/sorc/oops
@@ -1 +1 @@
-Subproject commit 47bf8d39a85b59f6694f66a1798597a27f8c3994
+Subproject commit e724cafc1615f74585a8a322cb9e60413f3bef91