WIP - Pylibs integration

notebooks/schism/demo_nml.yaml

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+output_dir: schism_declaritive
+period:
+  start: 20230101T00
+  end: 20230101T12
+  interval: 3600
+run_id: test_schism_nml
+delete_existing: True
+config:
+  model_type: schism
+  grid:
+    grid_type: schism
+    hgrid:
+      id: hgrid
+      model_type: data_blob
+       #source: ../../tests/schism/test_data/hgrid.gr3
+      source: ../../tests/schism/test_data/hgrid_20kmto60km_rompyschism_testing.gr3
+    # vgrid:
+    #   model_type: vgrid2D_generator
+    drag: 1
+  data:
+    data_type: schism
+    atmos:
+      air_1:
+        data_type: sflux_air
+        source: 
+          model_type: file
+          uri: "../../tests/schism/test_data/era5.nc"
+        uwind_name: u10
+        vwind_name: v10
+        prmsl_name: msl
+        filter:
+          sort: {coords: [latitude]}
+        buffer: 5
+    ocean:
+      elev2D:
+        buffer: 0.0
+        coords:
+          t: time
+          x: xlon
+          y: ylat
+        source: 
+          uri:  ../../tests/schism/test_data/hycom.nc
+          model_type: file
+        variables: 
+          - surf_el
+    tides:
+      data_type: tides
+      constituents: [M2, S2, N2]
+      flags: [[5, 3, 0, 0]]
+      tidal_database: "tpxo"
+      ntip: 0
+      cutoff_depth: 50.0
+      tidal_data:
+        data_type: tidal_dataset
+        elevations: ../../tests/schism/test_data/tpxo9-neaus/h_m2s2n2.nc
+        velocities: ../../tests/schism/test_data/tpxo9-neaus/u_m2s2n2.nc
+    wave:
+      buffer: 0.0
+      coords:
+        t: time
+        x: lon
+        y: lat
+        z: depth
+      id: wavedata
+      source:
+        catalog_uri: ../../tests/data/catalog.yaml
+        dataset_id: ausspec
+        model_type: intake
+  nml:
+    param:
+      schout:
+        iof_hydro__1: 1 # elevation
+        iof_hydro__2: 1 # mslp
+        iof_hydro__14: 1 # wind speed
+        iof_hydro__16: 1 # surface velocities
+        iof_wwm__18: 1 # peak wave direction
+        iof_wwm__1: 1 # significant wave height
+        iof_wwm__9: 1 # peak period
+    wwminput:
+      proc:
+        deltc: 100

notebooks/schism/demo_nml_3d_nontidal_velocities.yaml

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+output_dir: schism_declaritive
+period:
+  start: 20230101T00
+  end: 20230101T12
+  interval: 3600
+run_id: test_schism_nml_3d_nontidal_velocities
+delete_existing: True
+config:
+  model_type: schism
+  grid:
+    grid_type: schism
+    hgrid:
+      id: hgrid
+      model_type: data_blob
+      source: ../../tests/schism/test_data/hgrid_20kmto60km_rompyschism_testing.gr3
+    drag: 1
+    vgrid:
+      source: ../../tests/schism/test_data/vgrid.in
+  data:
+    data_type: schism
+    atmos:
+      air_1:
+        data_type: sflux_air
+        source: 
+          model_type: file
+          uri: "../../tests/schism/test_data/era5.nc"
+        uwind_name: u10
+        vwind_name: v10
+        prmsl_name: msl
+        filter:
+          sort: {coords: [latitude]}
+        buffer: 5
+    ocean:
+      elev2D:
+        buffer: 0.0
+        coords:
+          t: time
+          x: xlon
+          y: ylat
+        source: 
+          model_type: file
+          uri: "../../tests/schism/test_data/hycom.nc"
+        variables: 
+          - surf_el
+      SAL_3D:
+        buffer: 0.0
+        coords:
+          t: time
+          x: xlon
+          y: ylat
+          z: depth
+        source: 
+          model_type: file
+          uri: "../../tests/schism/test_data/hycom.nc"
+        variables: 
+         - salinity
+      uv3D:
+        buffer: 0.0
+        coords:
+          t: time
+          x: xlon
+          y: ylat
+          z: depth
+        source: 
+          model_type: file
+          uri:  ../../tests/schism/test_data/hycom.nc
+        variables: 
+          - water_u
+          - water_v
+      TEM_3D:
+        buffer: 0.0
+        coords:
+          t: time
+          x: xlon
+          y: ylat
+          z: depth
+        source: 
+          model_type: file
+          uri: "../../tests/schism/test_data/hycom.nc"
+        variables: 
+          - temperature
+    hotstart:
+      source: 
+        model_type: file
+        uri: "../../tests/schism/test_data/hycom.nc"
+      temp_var: temperature
+      salt_var: salinity
+      coords:
+        t: time
+        x: xlon
+        y: ylat
+        z: depth
+    tides:
+      constituents:
+      - M2
+      - S2
+      - N2
+      cutoff_depth: 50.0
+      flags: 
+        - [5, 3, 4, 4]
+      tidal_data:
+        data_type: tidal_dataset
+        elevations: ../../tests/schism/test_data/tpxo9-neaus/h_m2s2n2.nc
+        velocities: ../../tests/schism/test_data/tpxo9-neaus/u_m2s2n2.nc
+    wave:
+      buffer: 0.0
+      coords:
+        t: time
+        x: lon
+        y: lat
+        z: depth
+      id: wavedata
+      source:
+        catalog_uri: ../../tests/data/catalog.yaml
+        dataset_id: ausspec
+        model_type: intake
+  nml:
+    param:
+      core:
+        ibc: 0
+        ibtp: 1
+      schout:
+        iof_hydro__1: 1 # elevation
+        iof_hydro__2: 1 # mslp
+        iof_hydro__14: 1 # wind speed
+        iof_hydro__16: 1 # surface velocities
+        iof_hydro__18: 1 # water temperature
+        iof_hydro__19: 1 # salinity
+        iof_wwm__18: 1 # peak wave direction
+        iof_wwm__1: 1 # significant wave height
+        iof_wwm__9: 1 # peak period
+    wwminput:
+      proc:
+        deltc: 100

notebooks/schism/demo_nml_3d_tidal_velocities.yaml

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+output_dir: schism_declaritive
+period:
+  start: 20230101T00
+  end: 20230101T12
+  interval: 3600
+run_id: test_schism_nml_3d_tidal_velocities
+delete_existing: True
+config:
+  model_type: schism
+  grid:
+    grid_type: schism
+    hgrid:
+      id: hgrid
+      model_type: data_blob
+      source: ../../tests/schism/test_data/hgrid_20kmto60km_rompyschism_testing.gr3
+    drag: 1
+    vgrid:
+      source: ../../tests/schism/test_data/vgrid.in
+  data:
+    data_type: schism
+    atmos:
+      air_1:
+        data_type: sflux_air
+        source: 
+          model_type: file
+          uri: "../../tests/schism/test_data/era5.nc"
+        uwind_name: u10
+        vwind_name: v10
+        prmsl_name: msl
+        filter:
+          sort: {coords: [latitude]}
+        buffer: 5
+    ocean:
+      elev2D:
+        buffer: 0.0
+        coords:
+          t: time
+          x: xlon
+          y: ylat
+        source: 
+          model_type: file
+          uri: "../../tests/schism/test_data/hycom.nc"
+        variables: 
+          - surf_el
+      SAL_3D:
+        buffer: 0.0
+        coords:
+          t: time
+          x: xlon
+          y: ylat
+          z: depth
+        source: 
+          model_type: file
+          uri: "../../tests/schism/test_data/hycom.nc"
+        variables: 
+         - salinity
+    hotstart:
+      temp_var: water_temp
+      salt_var: salinity
+      coords:
+        t: time
+        x: xlon
+        y: ylat
+        z: depth
+
+      # uv3d:
+      #   buffer: 0.0
+      #   coords:
+      #     t: time
+      #     x: xlon
+      #     y: ylat
+      #     z: depth
+      #   source: 
+      #     model_type: file
+      #     uri:  ../../tests/schism/test_data/hycom.nc
+      #   variables: 
+      #     - water_u
+      #     - water_v
+      TEM_3D:
+        buffer: 0.0
+        coords:
+          t: time
+          x: xlon
+          y: ylat
+          z: depth
+        source: 
+          model_type: file
+          uri: "../../tests/schism/test_data/hycom.nc"
+        variables: 
+          - temperature
+    tides:
+      constituents:
+      - M2
+      - S2
+      - N2
+      cutoff_depth: 50.0
+      flags: 
+        - [5, 3, 4, 4]
+      tidal_data:
+        data_type: tidal_dataset
+        elevations: ../../tests/schism/test_data/tpxo9-neaus/h_m2s2n2.nc
+        velocities: ../../tests/schism/test_data/tpxo9-neaus/u_m2s2n2.nc
+    wave:
+      buffer: 0.0
+      coords:
+        t: time
+        x: lon
+        y: lat
+        z: depth
+      id: wavedata
+      source:
+        catalog_uri: ../../tests/data/catalog.yaml
+        dataset_id: ausspec
+        model_type: intake
+  nml:
+    param:
+      core:
+        ibc: 0
+        ibtp: 1
+      schout:
+        iof_hydro__1: 1 # elevation
+        iof_hydro__2: 1 # mslp
+        iof_hydro__14: 1 # wind speed
+        iof_hydro__16: 1 # surface velocities
+        iof_hydro__18: 1 # water temperature
+        iof_hydro__19: 1 # salinity
+        iof_wwm__18: 1 # peak wave direction
+        iof_wwm__1: 1 # significant wave height
+        iof_wwm__9: 1 # peak period
+    wwminput:
+      proc:
+        deltc: 100