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Marine B-matrix refactor companion PR #1346

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merged 28 commits into from
Nov 6, 2024
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d39bf61
Update jcb-gdas hash
DavidNew-NOAA Sep 27, 2024
1fde562
Update
DavidNew-NOAA Oct 7, 2024
12633b1
Merge branch 'develop' into feature/jcb-obsbias
DavidNew-NOAA Oct 7, 2024
3bf7b50
Update JCB gdas hash
DavidNew-NOAA Oct 8, 2024
8a501f7
Update jjob tests for new feature
DavidNew-NOAA Oct 8, 2024
29696c8
Change the way obs biases are staged
DavidNew-NOAA Oct 9, 2024
140dc0e
update jcb-gdas hash
DavidNew-NOAA Oct 9, 2024
c71d3b1
Merge branch 'develop' into feature/jcb-obsbias
DavidNew-NOAA Oct 13, 2024
6e85be0
Update JCB hash
DavidNew-NOAA Oct 13, 2024
c9fd183
Update marine JCB stuff
DavidNew-NOAA Oct 15, 2024
b706526
Merge branch 'feature/jcb-obsbias' into feature/marine-refactor
DavidNew-NOAA Oct 15, 2024
52bc8d5
Saving progress
DavidNew-NOAA Oct 15, 2024
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Merge branch 'develop' into feature/marine-refactor
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Merge branch 'develop' into feature/marine-refactor
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Merge branch 'develop' into feature/marine-refactor
DavidNew-NOAA Oct 22, 2024
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Merge branch 'develop' into feature/marine-refactor
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Remove some unnecessary lines
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Update JCB-GDAS hash
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Update JCB GDAS hash
DavidNew-NOAA Oct 23, 2024
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DavidNew-NOAA Oct 24, 2024
1264398
Remove YAMLs that are now in jcb-gdas
DavidNew-NOAA Oct 24, 2024
9be49de
Merge branch 'develop' into feature/marine-refactor
DavidNew-NOAA Oct 28, 2024
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Merge branch 'develop' into feature/marine-refactor
DavidNew-NOAA Oct 31, 2024
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Update jcb-gdas hash
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Update jcb-gdas branch
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Merge branch 'develop' into feature/marine-refactor
DavidNew-NOAA Nov 3, 2024
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2 changes: 1 addition & 1 deletion parm/jcb-gdas
Submodule jcb-gdas updated 32 files
+33 −0 .github/workflows/run_jcb_basic_testing.yaml
+48 −0 algorithm/aero/aero_convert_background.yaml.j2
+81 −0 algorithm/aero/aero_gen_bmatrix_diagb.yaml.j2
+48 −0 algorithm/aero/aero_gen_bmatrix_diffusion.yaml.j2
+37 −0 algorithm/marine/soca_diagb.yaml.j2
+98 −0 algorithm/marine/soca_ensb.yaml.j2
+37 −0 algorithm/marine/soca_ensweights.yaml.j2
+5 −0 algorithm/marine/soca_gridgen.yaml.j2
+37 −0 algorithm/marine/soca_parameters_diffusion_hz.yaml.j2
+33 −0 algorithm/marine/soca_parameters_diffusion_vt.yaml.j2
+23 −0 algorithm/marine/soca_setcorscales.yaml.j2
+13 −0 algorithm/marine/soca_vtscales.yaml.j2
+1 −0 model/aero/aero_3dfgat_outer_loop_1.yaml.j2
+1 −0 model/aero/aero_3dfgat_outer_loop_2.yaml.j2
+17 −0 model/aero/aero_3dvar_outer_loop_1.yaml.j2
+17 −0 model/aero/aero_3dvar_outer_loop_2.yaml.j2
+10 −0 model/aero/aero_background.yaml.j2
+33 −0 model/aero/aero_background_error_static_diffusion.yaml.j2
+23 −0 model/aero/aero_final_increment_cubed_sphere.yaml.j2
+18 −0 model/aero/aero_final_increment_gaussian.yaml.j2
+0 −0 model/aero/aero_geometry.yaml.j2
+11 −0 model/aero/aero_geometry_background.yaml.j2
+13 −0 model/aero/aero_model_pseudo.yaml.j2
+0 −0 observation_chronicle/atmosphere/iasi_metop-a.yaml
+0 −0 observation_chronicle/atmosphere/iasi_metop-b.yaml
+63 −0 observations/aero/viirs_n20_aod.yaml.j2
+63 −0 observations/aero/viirs_n21_aod.yaml.j2
+63 −0 observations/aero/viirs_npp_aod.yaml.j2
+31 −89 observations/atmosphere-lgetkf/iasi_metop-a.yaml.j2
+31 −89 observations/atmosphere-lgetkf/iasi_metop-b.yaml.j2
+31 −90 observations/atmosphere/iasi_metop-a.yaml.j2
+31 −90 observations/atmosphere/iasi_metop-b.yaml.j2
37 changes: 0 additions & 37 deletions parm/soca/berror/soca_diagb.yaml.j2

This file was deleted.

98 changes: 0 additions & 98 deletions parm/soca/berror/soca_ensb.yaml.j2

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37 changes: 0 additions & 37 deletions parm/soca/berror/soca_ensweights.yaml.j2

This file was deleted.

37 changes: 0 additions & 37 deletions parm/soca/berror/soca_parameters_diffusion_hz.yaml.j2

This file was deleted.

33 changes: 0 additions & 33 deletions parm/soca/berror/soca_parameters_diffusion_vt.yaml.j2

This file was deleted.

23 changes: 0 additions & 23 deletions parm/soca/berror/soca_setcorscales.yaml

This file was deleted.

13 changes: 0 additions & 13 deletions parm/soca/berror/soca_vtscales.yaml.j2

This file was deleted.

9 changes: 6 additions & 3 deletions parm/soca/marine-jcb-base.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,7 @@ final_increment_file: marine_final_increment

# Assimilation standard things (not prepended with model choice)
# ----------------------------
window_begin: '{{MARINE_WINDOW_BEGIN}}'
window_begin: '{{ MARINE_WINDOW_BEGIN | to_isotime }}'
window_length: '{{MARINE_WINDOW_LENGTH}}'
bound_to_include: begin
minimizer: RPCG
Expand All @@ -31,6 +31,10 @@ analysis_variables: [cicen, hicen, hsnon, socn, tocn, uocn, vocn, ssh]
# ------------
marine_window_begin: '{{MARINE_WINDOW_BEGIN}}'
marine_window_middle: '{{MARINE_WINDOW_MIDDLE}}'
marine_window_begin_iso: '{{ MARINE_WINDOW_BEGIN | to_isotime }}'
marine_window_middle_iso: '{{ MARINE_WINDOW_MIDDLE | to_isotime }}'
marine_window_end_iso: '{{ MARINE_WINDOW_END | to_isotime }}'
enspert_relpath: '{{ ENSPERT_RELPATH }}'

# Geometry
marine_soca_files_path: .
Expand All @@ -42,11 +46,10 @@ marine_background_time: '{{MARINE_WINDOW_BEGIN_ISO}}'

# Pseudo model
marine_forecast_timestep: PT3H
marine_pseudo_model_states: !INC 'bkg_list.yaml'

# Background error model
background_error_file: '{{berror_model}}'
marine_number_ensemble_members: '{{nmem_ens}}'
marine_number_ensemble_members: '{{NMEM_ENS}}'
marine_stddev_time: '{{MARINE_WINDOW_MIDDLE}}'

# Observations
Expand Down
2 changes: 0 additions & 2 deletions parm/soca/soca_fix_stage_500.yaml.j2
Original file line number Diff line number Diff line change
Expand Up @@ -9,8 +9,6 @@ copy:
- ["{{ SOCA_INPUT_FIX_DIR }}/field_table", "{{ DATA }}/field_table"]
- ["{{ SOCA_INPUT_FIX_DIR }}/diag_table", "{{ DATA }}/diag_table"]
- ["{{ SOCA_INPUT_FIX_DIR }}/MOM_input", "{{ DATA }}/MOM_input"]
- ["{{ SOCA_INPUT_FIX_DIR }}/fields_metadata.yaml", "{{ DATA }}/fields_metadata.yaml"]
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- ["{{ SOCA_INPUT_FIX_DIR }}/obsop_name_map.yaml", "{{ DATA }}/obsop_name_map.yaml"]
- ["{{ SOCA_INPUT_FIX_DIR }}/INPUT/grid_spec.nc", "{{ DATA }}/INPUT/grid_spec.nc"]
- ["{{ SOCA_INPUT_FIX_DIR }}/INPUT/hycom1_25.nc", "{{ DATA }}/INPUT/hycom1_25.nc"]
- ["{{ SOCA_INPUT_FIX_DIR }}/INPUT/layer_coord25.nc", "{{ DATA }}/INPUT/layer_coord25.nc"]
Expand Down
1 change: 0 additions & 1 deletion parm/soca/soca_utils_stage.yaml.j2
Original file line number Diff line number Diff line change
Expand Up @@ -4,4 +4,3 @@
copy:
- ["{{ HOMEgfs }}/parm/gdas/soca/fields_metadata.yaml", "{{ DATA }}/fields_metadata.yaml"]
- ["{{ HOMEgfs }}/parm/gdas/soca/obsop_name_map.yaml", "{{ DATA }}/obsop_name_map.yaml"]
- ["{{ HOMEgfs }}/parm/gdas/soca/gridgen/gridgen.yaml", "{{ DATA }}/gridgen.yaml"]
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