Leaf Age Response function for all Biogenic VOCs consistent with MEGAN #92
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -882,6 +882,63 @@ | |
| "source": [ | ||
| "ds.emi_apin.mean(\"z\", keep_attrs=True).plot(size=4, marker=\"o\")" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "id": "0a445f3c-52a2-4a3f-89be-c06011b91a76", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "### Leaf age parameterization" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "id": "a0eee654-2333-408e-a4f6-0bb9ed574600", | ||
| "metadata": { | ||
| "tags": [] | ||
| }, | ||
| "outputs": [], | ||
| "source": [ | ||
| "config = {\n", | ||
| " \"filenames\": {\n", | ||
| " \"file_vars\": [\n", | ||
| " \"../input/point_file_20220630.sfcf023.txt\",\n", | ||
| " \"../input/point_file_20220701.sfcf000.txt\",\n", | ||
| " \"../input/point_file_20220701.sfcf001.txt\",\n", | ||
| " ],\n", | ||
| " },\n", | ||
| " \"userdefs\": {\n", | ||
| " \"infmt_opt\": 1,\n", | ||
| " \"ntime\": 3,\n", | ||
| " \"nlat\": 1,\n", | ||
| " \"nlon\": 1,\n", | ||
| " \"leafage_opt\": 0, # on\n", | ||
| " },\n", | ||
| "}\n", | ||
| "ds0 = run(config=config)\n", | ||
| "\n", | ||
| "config[\"userdefs\"][\"leafage_opt\"] = 1 # off\n", | ||
| "ds1 = run(config=config)\n", | ||
| "\n", | ||
| "ds = xr.concat([ds0, ds1], dim=\"leafage_opt\")\n", | ||
| "ds" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "id": "2439516f-bd60-495f-bbc5-5dfe70555c03", | ||
| "metadata": { | ||
| "tags": [] | ||
| }, | ||
| "outputs": [], | ||
| "source": [ | ||
| "fig, [ax1, ax2] = plt.subplots(2, 1, figsize=(5, 6), sharex=True)\n", | ||
| "\n", | ||
| "ds.emi_apin.mean(\"z\", keep_attrs=True).plot(hue=\"leafage_opt\", marker=\"o\", ax=ax1)\n", | ||
| "ds.emi_isop.mean(\"z\", keep_attrs=True).plot(hue=\"leafage_opt\", marker=\"o\", ax=ax2)" | ||
| ] | ||
| } | ||
| ], | ||
| "metadata": { | ||
|
|
@@ -900,7 +957,7 @@ | |
| "name": "python", | ||
| "nbconvert_exporter": "python", | ||
| "pygments_lexer": "ipython3", | ||
| "version": "3.11.5" | ||
| } | ||
| }, | ||
| "nbformat": 4, | ||
|
|
||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,5 +1,6 @@ | ||
| """ | ||
| Created on Sun Jun 4 2023 | ||
| Updated on Mon Oct 16 2023: Use daily gfs.canopy files | ||
|
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| Author: Wei-Ting Hung | ||
| """ | ||
|
|
@@ -14,7 +15,7 @@ | |
| from scipy.interpolate import griddata | ||
|
|
||
| """User Options""" | ||
| path = "/scratch1/BMC/rcm2/qrasool/canopy-app-LeafAgeTimeFeature/input" # "/scratch/pcampbe8/canopy-app/input" # work directory | ||
| year = 2022 # year | ||
| month = 7 # month | ||
| day = 1 # day | ||
|
|
@@ -65,7 +66,7 @@ | |
| f_met = ( | ||
| path + "/gfs.t" + HHI + "z." + YY + MM + DD + ".sfcf0" + HH + ".nc" | ||
| ) # gfs met file | ||
| f_can = path + "/gfs.canopy.t" + HHI + "z." + YY + MM + DD + ".sfcf000.nc" # canopy file | ||
| f_output = ( | ||
| path + "/gfs.canopy.t" + HHI + "z." + YY + MM + DD + ".global.f0" + HH + ".nc" | ||
| ) # output file | ||
|
|
@@ -88,7 +89,7 @@ | |
| + ".nc " | ||
| ) | ||
| elif frp_src == 2: # climatological frp | ||
| f_frp = path + "/gfs.canopy.t" + HHI + "z." + YY + MM + DD + ".sfcf000.nc" | ||
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|
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| # required variables | ||
|
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@@ -109,7 +110,7 @@ | |
| "hpbl", | ||
| "prate_ave", | ||
| ] | ||
| canlist = ["lai", "clu", "ffrac", "fh", "pavd", "mol", "csz", "frp", "href"] | ||
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||
|
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| # constants | ||
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@@ -149,12 +150,35 @@ def mapping(xgrid, ygrid, data, xdata, ydata, map_method, fvalue): | |
| def read_gfs_climatology(filename, lat, lon, varname): | ||
| readin = Dataset(filename) | ||
|
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||
| if varname == "pavd": | ||
| # map to met grids | ||
| yt = readin["lat"][:] | ||
| xt = readin["lon"][:] | ||
| data = np.squeeze(readin[varname][:]) | ||
|
|
||
| DATA = np.empty([data.shape[0], lat.shape[0], lat.shape[1]]) | ||
|
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||
| for ll in np.arange(data.shape[0]): | ||
| DATA[ll, :, :] = mapping( | ||
| lat, | ||
| lon, | ||
| data[ll, :, :].flatten(), | ||
| yt.flatten(), | ||
| xt.flatten(), | ||
| "linear", | ||
| np.nan, | ||
| ) | ||
|
|
||
| else: | ||
| # map to met grids | ||
| yt = readin["lat"][:] | ||
| xt = readin["lon"][:] | ||
| data = np.squeeze(readin[varname][0, :, :]) | ||
|
|
||
| DATA = mapping( | ||
| lat, lon, data.flatten(), yt.flatten(), xt.flatten(), "linear", np.nan | ||
| ) | ||
|
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| DATA[np.isnan(DATA)] = 0 | ||
| DATA[DATA < 0] = 0 | ||
| return DATA | ||
|
|
@@ -226,7 +250,8 @@ def read_frp_local(filename, lat, lon, fill_value): | |
| + "z." | ||
| + YY | ||
| + MM | ||
| + DD | ||
| + ".sfcf000.nc", | ||
| ] | ||
| ) | ||
| if os.path.isfile(f_can) is True: | ||
|
|
@@ -262,7 +287,7 @@ def read_frp_local(filename, lat, lon, fill_value): | |
| else: | ||
| print("---- No available FRP file. Switch to Climatology FRP...") | ||
| frp_src = 2 | ||
| f_frp = path + "/gfs.canopy.t" + HHI + "z." + YY + MM + DD + ".sfcf000.nc" | ||
|
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| if frp_src == 2: # 12 month climatology frp | ||
| if os.path.isfile(f_frp) is True: | ||
|
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@@ -281,7 +306,8 @@ def read_frp_local(filename, lat, lon, fill_value): | |
| + "z." | ||
| + YY | ||
| + MM | ||
| + DD | ||
| + ".sfcf000.nc", | ||
| ] | ||
| ) | ||
| if os.path.isfile(f_met) is True: | ||
|
|
@@ -354,6 +380,11 @@ def read_frp_local(filename, lat, lon, fill_value): | |
| ATT = ["Canopy height above the surface", "m", fill_value] | ||
| DATA = read_gfs_climatology(f_can, lat, lon, "fh") | ||
|
|
||
| elif varname == "pavd": | ||
| ATTNAME = ["long_name", "units", "missing_value"] | ||
| ATT = ["Plant area volume density profile", "m2/m3", fill_value] | ||
| DATA = read_gfs_climatology(f_can, lat, lon, "pavd") | ||
|
|
||
| elif varname == "mol": | ||
| # Reference: | ||
| # Essa 1999, ESTIMATION OF MONIN-OBUKHOV LENGTH USING RICHARDSON AND BULK RICHARDSON NUMBER | ||
|
|
@@ -409,15 +440,48 @@ def read_frp_local(filename, lat, lon, fill_value): | |
| print(ATT) | ||
|
|
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| # adding to output file | ||
| if varname == "pavd": | ||
| output = Dataset(f_output, "a") | ||
| output.createDimension("level", DATA.shape[0]) | ||
|
|
||
| var_bot = output.createVariable("layer_bottom", "i4", ("level",)) | ||
| var_top = output.createVariable("layer_top", "i4", ("level",)) | ||
| var = output.createVariable( | ||
| varname, | ||
| "float", | ||
| ("time", "level", "grid_yt", "grid_xt"), | ||
| fill_value=fill_value, | ||
| ) | ||
|
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| write_varatt(var, ATTNAME, ATT) | ||
| write_varatt( | ||
| var_bot, | ||
| ["long_name", "units"], | ||
| ["height of the layer bottom above the ground", "m"], | ||
| ) | ||
| write_varatt( | ||
| var_top, | ||
| ["long_name", "units"], | ||
| ["height of the layer top above the ground", "m"], | ||
| ) | ||
|
|
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| var_bot[:] = np.arange(0, 65 + 1, 5) | ||
| var_top[:] = np.arange(5, 70 + 1, 5) | ||
| var[:] = DATA | ||
|
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| output.close() | ||
| del [var_bot, var_top] | ||
|
|
||
| else: | ||
| output = Dataset(f_output, "a") | ||
|
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| var = output.createVariable( | ||
| varname, "float", ("time", "grid_yt", "grid_xt"), fill_value=fill_value | ||
| ) | ||
| write_varatt(var, ATTNAME, ATT) | ||
| var[:] = DATA | ||
|
|
||
| output.close() | ||
|
|
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| print("---- " + varname + " complete!") | ||
|
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||
|
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||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -85,7 +85,7 @@ program canopy_app | |
| ! Main canopy model calculations. | ||
| !------------------------------------------------------------------------------- | ||
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| call canopy_calcs(nn) | ||
|
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| !------------------------------------------------------------------------------- | ||
| ! Write model output of canopy model calculations. | ||
|
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@quaz115 Please also revert these input files back to what they are in default [develop] branch. Thanks!
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this should be uncommented right: file_vars = 'input/gfs.t12z.20220630.sfcf023.canopy.nc' 'input/gfs.t12z.20220701.sfcf000.canopy.nc' 'input/gfs.t12z.20220701.sfcf001.canopy.nc'
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Should look like this: