Update variables for v3 ELM

e3sm_to_cmip/cmor_handlers/_formulas.py

@@ -580,8 +580,44 @@ def rtmt(ds: xr.Dataset) -> xr.DataArray:
 
 def tran(ds: xr.Dataset) -> xr.DataArray:
     """
-    tran = QSOIL + QVEGT
+    tran = QVEGT
     """
-    result = ds["QSOIL"] + ds["QVEGT"]
+    result = ds["QVEGT"]
+
+    return result
+
+
+def burntFractionAll(ds: xr.Dataset) -> xr.DataArray:
+    """
+    burntFractionAll = FAREA_BURNED*3600*24*30*100
+    """
+    result = ds["FAREA_BURNED"] * 3600 * 24 * 30 * 100
+
+    return result
+
+
+def cRoot(ds: xr.Dataset) -> xr.DataArray:
+    """
+    cRoot = (FROOTC+LIVECROOTC+DEADCROOTC)/1000
+    """
+    result = (ds["FROOTC"] + ds["LIVECROOTC"] + ds["DEADCROOTC"]) / 1000
+
+    return result
+
+
+def rGrowth(ds: xr.Dataset) -> xr.DataArray:
+    """
+    rGrowth = (AR-MR)/1000
+    """
+    result = (ds["AR"] - ds["MR"]) / 1000
+
+    return result
+
+
+def sootsn(ds: xr.Dataset) -> xr.DataArray:
+    """
+    sootsn = SNOBCMSL+SNODSTMSL+SNOOCMSL
+    """
+    result = ds["SNOBCMSL"] + ds["SNODSTMSL"] + ds["SNOOCMSL"]
 
     return result

e3sm_to_cmip/cmor_handlers/handlers.yaml

@@ -31,6 +31,134 @@
   formula: null
   positive: null
   levels: null
+- name: burntFractionAll
+  units: "%"
+  raw_variables: [FAREA_BURNED]
+  table: CMIP6_Lmon.json
+  unit_conversion: null
+  formula: FAREA_BURNED*3600*24*30*100
+  positive: null
+  levels: null
+- name: cCwd
+  units: kg m-2
+  raw_variables: [CWDC]
+  table: CMIP6_Lmon.json
+  unit_conversion: g-to-kg
+  formula: null
+  positive: null
+  levels: null
+- name: cLeaf
+  units: kg m-2
+  raw_variables: [LEAFC]
+  table: CMIP6_Lmon.json
+  unit_conversion: g-to-kg
+  formula: null
+  positive: null
+  levels: null
+- name: cRoot
+  units: kg m-2
+  raw_variables: [FROOTC, LIVECROOTC, DEADCROOTC]
+  table: CMIP6_Lmon.json
+  unit_conversion: null
+  formula: (FROOTC+LIVECROOTC+DEADCROOTC)/1000
+  positive: null
+  levels: null
+- name: hfdsn
+  units: W m-2
+  raw_variables: [FGR]
+  table: CMIP6_LImon.json
+  unit_conversion: "-1"
+  formula: null
+  positive: down
+  levels: null
+- name: lwsnl
+  units: kg m-2
+  raw_variables: [SNOWLIQ]
+  table: CMIP6_LImon.json
+  unit_conversion: null
+  formula: null
+  positive: null
+  levels: null
+- name: nppLeaf
+  units: kg m-2 s-1
+  raw_variables: [LEAFC_ALLOC]
+  table: CMIP6_Lmon.json
+  unit_conversion: null
+  formula: null
+  positive: down
+  levels: null
+- name: nppRoot
+  units: kg m-2 s-1
+  raw_variables: [FROOTC_ALLOC]
+  table: CMIP6_Lmon.json
+  unit_conversion: g-to-kg
+  formula: null
+  positive: down
+  levels: null
+- name: nppWood
+  units: kg m-2 s-1
+  raw_variables: [WOODC_ALLOC]
+  table: CMIP6_Lmon.json
+  unit_conversion: g-to-kg
+  formula: null
+  positive: down
+  levels: null
+- name: rGrowth
+  units: kg m-2 s-1
+  raw_variables: [AR, MR]
+  table: CMIP6_Lmon.json
+  unit_conversion: null
+  formula: (AR-MR)/1000
+  positive: down
+  levels: null
+- name: rMaint
+  units: kg m-2 s-1
+  raw_variables: [MR]
+  table: CMIP6_Lmon.json
+  unit_conversion: g-to-kg
+  formula: null
+  positive: down
+  levels: null
+- name: snc
+  units: "%"
+  raw_variables: [FSNO]
+  table: CMIP6_LImon.json
+  unit_conversion: 1-to-%
+  formula: null
+  positive: null
+  levels: null
+- name: snd
+  units: m
+  raw_variables: [SNOWDP]
+  table: CMIP6_LImon.json
+  unit_conversion: null
+  formula: null
+  positive: null
+  levels: null
+- name: snm
+  units: kg m-2 s-1
+  raw_variables: [QSNOMELT]
+  table: CMIP6_LImon.json
+  unit_conversion: null
+  formula: null
+  positive: null
+  levels: null
+- name: snw
+  units: kg m-2
+  raw_variables: [H2OSNO_TOP]
+  table: CMIP6_LImon.json
+  unit_conversion: null
+  formula: null
+  positive: null
+  levels: null
+- name: sootsn
+  units: kg m-2
+  raw_variables: [SNOBCMSL, SNODSTMSL, SNOOCMSL]
+  table: CMIP6_LImon.json
+  unit_conversion: null
+  formula: SNOBCMSL+SNODSTMSL+SNOOCMSL
+  positive: null
+  levels: null
 - name: albisccp
   units: "1"
   raw_variables: [MEANCLDALB_ISCCP]
@@ -980,10 +1108,10 @@
   levels: null
 - name: tran
   units: kg m-2 s-1
-  raw_variables: [QVEGT, QSOIL]
+  raw_variables: [QVEGT]
   table: CMIP6_Lmon.json
   unit_conversion: null
-  formula: QSOIL + QVEGT
+  formula: QVEGT
   positive: up
   levels: null
 - name: ts

e3sm_to_cmip/mpas.py

@@ -802,19 +802,26 @@ def _compute_moc_time_series(
             ).sum(dim="nCells")
             mocSlices.append(mocTop)
 
-        moc = xarray.concat(mocSlices, dim="lat")  # type: ignore
-        moc = moc.transpose("Time", "nVertLevelsP1", "lat")  # type: ignore
+        moc = xarray.concat(mocSlices, dim="lat")  # type: ignore[arg-type]
+        moc = moc.transpose("Time", "nVertLevelsP1", "lat")
+
         # average to bin and level centers
-        moc = 0.25 * (
-            moc[:, 0:-1, 0:-1] + moc[:, 0:-1, 1:] + moc[:, 1:, 0:-1] + moc[:, 1:, 1:]
+        moc_avg = (
+            0.25
+            * (
+                moc[:, 0:-1, 0:-1]  # type: ignore[index]
+                + moc[:, 0:-1, 1:]  # type: ignore[index]
+                + moc[:, 1:, 0:-1]  # type: ignore[index]
+                + moc[:, 1:, 1:]  # type: ignore[index]
+            )
         )
-        moc = moc.rename({"nVertLevelsP1": "depth"})  # type: ignore
-        binCounts = xarray.DataArray(binCounts, dims=("lat"))  # type: ignore
-        moc = moc.where(binCounts > 0)  # type: ignore
+        moc_avg = moc_avg.rename({"nVertLevelsP1": "depth"})
+        binCounts = xarray.DataArray(binCounts, dims=("lat"))  # type: ignore[assignment]
+        moc_masked = moc_avg.where(binCounts > 0)  # type: ignore[operator]
 
-        _compute_dask(moc, showProgress, "Computing {} MOC".format(regionName))
+        _compute_dask(moc_masked, showProgress, "Computing {} MOC".format(regionName))
 
-        mocs[regionName] = moc
+        mocs[regionName] = moc_masked
 
     mocs = xarray.concat(mocs.values(), dim="basin")  # type: ignore
     mocs = mocs.transpose("Time", "basin", "depth", "lat")  # type: ignore

e3sm_to_cmip/runner.py

@@ -323,7 +323,7 @@ def _get_e3sm_vars(self, input_path: str) -> list[str]:
 
         for path in paths:
             ds = xr.open_dataset(path, decode_timedelta=True)
-            data_vars = list(ds.data_vars.keys())
+            data_vars = [str(var) for var in ds.data_vars.keys()]
 
             e3sm_vars = e3sm_vars + data_vars
 

scripts/debug/334-new_v3_land_handlers/run_v3_land.sh

@@ -0,0 +1,55 @@
+#!/bin/bash
+
+# Conda Environment
+# -----------------
+#conda activate e3sm_to_cmip_dev
+
+# -----------------
+# PATHS
+# -----------------
+e2c_path=/lcrc/group/e3sm/public_html/diagnostics/e3sm_to_cmip_data
+model_data=/gpfs/fs0/globalscratch/ac.zhang40/e2c_tests/model_data
+scratch=/gpfs/fs0/globalscratch/ac.zhang40
+
+# TODO: Update result_dir
+result_dir=${scratch}/e2c_tests
+
+rgr_dir=${result_dir}/rgr
+rgr_dir_vert=${result_dir}/rgr_vert
+rgr_dir_vert_plev=${result_dir}/rgr_vert_plev
+native_dir=${result_dir}/native
+
+map_file=${e2c_path}/maps/map_r05_to_cmip6_180x360_traave.20231110.nc
+tables_path=${e2c_path}/cmip6-cmor-tables/Tables/
+metadata_path=${e2c_path}/default_metadata.json
+
+start=1850
+end=1850
+ypf=1
+caseid=v3.LR.historical_0101
+
+## ------------------------------------------------------
+## TEST CASE - land monthly h0
+## ------------------------------------------------------
+#input_path=${model_data}/
+input_path=/lcrc/group/e3sm2/ac.wlin/E3SMv3/v3.LR.historical_0101/archive/lnd/hist
+flags='-7 --dfl_lvl=1 --no_cll_msr'
+#raw_var_list="LAISHA,LAISUN,QINTR,QOVER,QRUNOFF,QSOIL,QVEGE,QVEGT,SOILICE,SOILLIQ,SOILWATER_10CM,TSA,TSOI,H2OSNO"
+#cmip_var_list="mrsos, mrso, mrfso, mrros, mrro, prveg, evspsblveg, evspsblsoi, tran, tsl, lai"
+raw_var_list="LEAFC,FROOTC,LIVECROOTC,DEADCROOTC,CWDC,AR,MR,QVEGT,LEAFC_ALLOC,FROOTC_ALLOC,WOODC_ALLOC,FAREA_BURNED,LAND_USE_FLUX,FSNO,SNOWDP,SNOWLIQ,H2OSNO_TOP,QSNOMELT,FGR,SNOBCMSL,SNODSTMSL,SNOOCMSL"
+cmip_var_list="burntFractionAll, cCwd, cLeaf, cRoot, nppLeaf, nppRoot, nppWood, rGrowth, rMaint, tran, hfdsn, lwsnl, snc, snd, snm, snw, sootsn"
+
+rgr_dir=${result_dir}/rgr_lnd
+native_dir=${result_dir}/native_lnd
+mkdir -p $rgr_dir
+mkdir -p $native_dir
+
+# Note either include the extra variable landfrac or specify the file that has landfrac for subgrid scale mode to work.
+#ncclimo -P elm -j 1 --var_xtr=landfrac --map=${map_file} --start=$start --end=$end --ypf=$ypf --split -c $caseid -o ${native_dir} -O ${rgr_dir} -v ${raw_var_list} -i ${input_path} ${flags}
+# Alternative ncclimo invocation
+#ncclimo -P elm -j 1 --map=${map_file} --start=$start --end=$end --ypf=$ypf --split -c $caseid -o ${native_dir} -O ${rgr_dir} -v ${raw_var_list} -i ${input_path} ${flags} --sgs_frc=${input_path}/v2.LR.historical_0101.elm.h0.1850-01.nc/landfrac
+
+#raw_var_list_elm_bgc="TOTLITC,CWDC,TOTPRODC,SOIL1C,SOIL2C,SOIL3C,^SOIL4C$,COL_FIRE_CLOSS,WOOD_HARVESTC,TOTVEGC,NBP,GPP,AR,HR"
+# CMORIZE Land Monthly variables
+e3sm_to_cmip -i ${rgr_dir} -o $result_dir  -v ${cmip_var_list} -t ${tables_path} -u ${metadata_path} --realm lnd --serial
+

tests/cmor_handlers/test__formulas.py

@@ -382,21 +382,19 @@ def test_rtmt():
 
     # Test when required variable keys are NOT in the data dictionary.
     with pytest.raises(KeyError):
-        rsuscs(xr.Dataset())
+        rtmt(xr.Dataset())
 
 
 def test_tran():
-    ds = xr.Dataset(
-        data_vars={"QSOIL": _dummy_dataarray(), "QVEGT": _dummy_dataarray()}
-    )
+    ds = xr.Dataset(data_vars={"QVEGT": _dummy_dataarray()})
 
     result = tran(ds)
     expected = xr.DataArray(
         dims=["lat", "lon"],
-        data=np.array([[0, 2, 4], [0, 2, 4], [0, 2, 4]]),
+        data=np.array([[0, 1, 2], [0, 1, 2], [0, 1, 2]]),
     )
     xr.testing.assert_allclose(result, expected)
 
     # Test when required variable keys are NOT in the data dictionary.
     with pytest.raises(KeyError):
-        rsuscs(xr.Dataset())
+        tran(xr.Dataset())