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. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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If not, see . + +Also add information on how to contact you by electronic and paper mail. + + If the program does terminal interaction, make it output a short +notice like this when it starts in an interactive mode: + + Copyright (C) + This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, your program's commands +might be different; for a GUI interface, you would use an "about box". + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU GPL, see +. + + The GNU General Public License does not permit incorporating your program +into proprietary programs. If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. 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