big fixes

fire/FatesFuelMod.F90

@@ -32,8 +32,8 @@ module FatesFuelMod
       procedure :: SumLoading
       procedure :: CalculateFractionalLoading
       procedure :: UpdateFuelMoisture
-      procedure :: AverageBulkDensity
-      procedure :: AverageSAV
+      procedure :: AverageBulkDensity_NoTrunks
+      procedure :: AverageSAV_NoTrunks
 
   end type fuel_type
 
@@ -302,7 +302,7 @@ real(r8) function MoistureOfExtinction(sav)
       real(r8), parameter :: MEF_b = 0.066_r8
 
       if (sav <= 0.0_r8) then
-        write(fates_log(), *) 'SAV cannot be negative - SAV = ' // sav
+        write(fates_log(), *) 'SAV cannot be negative - SAV'
         call endrun(msg=errMsg(__FILE__, __LINE__))
       else
         MoistureOfExtinction = MEF_a - MEF_b*log(sav)

fire/SFParamsMod.F90

@@ -32,7 +32,7 @@ module SFParamsMod
    real(r8),protected, public :: SF_val_SAV(num_fuel_classes)
    real(r8),protected, public :: SF_val_FBD(num_fuel_classes)
    real(r8),protected, public :: SF_val_min_moisture(num_fuel_classes)
-   real(r8),protected, public :: SF_val_mid_moisture(NFSC)
+   real(r8),protected, public :: SF_val_mid_moisture(num_fuel_classes)
    real(r8),protected, public :: SF_val_low_moisture_Coeff(num_fuel_classes)
    real(r8),protected, public :: SF_val_low_moisture_Slope(num_fuel_classes)
    real(r8),protected, public :: SF_val_mid_moisture_Coeff(num_fuel_classes)

testing/CMakeLists.txt

@@ -3,8 +3,8 @@
 ## Functional tests
 add_subdirectory(functional_testing/allometry fates_allom_ftest)
 add_subdirectory(functional_testing/math_utils fates_math_ftest)
-add_subdirectory(functional_testing/fire fates_fuel_test)
+add_subdirectory(functional_testing/fire fates_fuel_ftest)
 
 ## Unit tests
 add_subdirectory(unit_testing/fire_weather_test fates_fire_weather_utest)
-add_subdirectory(unit_testing/fire_fuel_test fates_fire_fuel_utest)
+add_subdirectory(unit_testing/fire_fuel_test fates_fire_fuel_utest)

testing/functional_testing/fire/FatesTestFuel.F90

@@ -91,8 +91,8 @@ program FatesTestFuel
     call fuel(f)%CalculateFractionalLoading()
 
     ! calculate geometric properties
-    call fuel(f)%AverageBulkDensity(SF_val_FBD)
-    call fuel(f)%AverageSAV(SF_val_SAV)
+    call fuel(f)%AverageBulkDensity_NoTrunks(SF_val_FBD)
+    call fuel(f)%AverageSAV_NoTrunks(SF_val_SAV)
 
     ! save values
     fuel_loading(:,f) = fuel(f)%loading(:)

testing/functional_testing/fire/fuel_test.py

@@ -0,0 +1,187 @@
+"""
+Concrete class for running the fuel functional test for FATES.
+"""
+import os
+import numpy as np
+import xarray as xr
+import matplotlib.pyplot as plt
+from functional_class import FunctionalTest
+
+
+class FuelTest(FunctionalTest):
+    """Fuel test class"""
+
+    name = "fuel"
+
+    def __init__(self, test_dict):
+        super().__init__(
+            FuelTest.name,
+            test_dict["test_dir"],
+            test_dict["test_exe"],
+            test_dict["out_file"],
+            test_dict["use_param_file"],
+            test_dict["other_args"],
+        )
+        self.plot = True
+
+    def plot_output(self, run_dir: str, save_figs: bool, plot_dir: str):
+        """Plot output associated with fuel tests
+
+        Args:
+            run_dir (str): run directory
+            out_file (str): output file
+            save_figs (bool): whether or not to save the figures
+            plot_dir (str): plot directory
+        """
+
+        fuel_dat = xr.open_dataset(os.path.join(run_dir, self.out_file))
+
+        self.plot_NI_dat(fuel_dat, save_figs, plot_dir)
+        self.plot_moisture_dat(fuel_dat, save_figs, plot_dir)
+        self.plot_barchart(
+            fuel_dat,
+            "fuel_loading",
+            "Fuel loading",
+            "kgC m$^{-2}$",
+            save_figs,
+            plot_dir,
+        )
+        self.plot_barchart(
+            fuel_dat,
+            "frac_loading",
+            "Fractional fuel loading",
+            "0-1",
+            save_figs,
+            plot_dir,
+        )
+        self.plot_barchart(
+            fuel_dat,
+            "bulk_density",
+            "Fuel bulk density",
+            "kg m$^{-3}$",
+            save_figs,
+            plot_dir,
+            by_litter_type=False,
+        )
+        self.plot_barchart(
+            fuel_dat,
+            "SAV",
+            "Fuel surface area to volume ratio",
+            "cm$^{-1}$",
+            save_figs,
+            plot_dir,
+            by_litter_type=False,
+        )
+
+    @staticmethod
+    def plot_barchart(
+        fuel_dat: xr.Dataset,
+        var: str,
+        varname: str,
+        units: str,
+        save_figs: bool,
+        plot_dir: bool,
+        by_litter_type: bool = True,
+    ):
+        """Plots fuel data output as a bar chart
+
+        Args:
+            fuel_dat (xr.Dataset): fuel data output
+            var (str): variable to plot
+            varname (str): variable name for x axis
+            units (str): units description
+            save_figs (bool): whether or not to save figure
+            plot_dir (bool): where to save figure
+            by_litter_type (bool, optional): whether the bar chart is by litter type. Defaults to True.
+        """
+
+        litter_classes = [
+            "twigs",
+            "small branches",
+            "large branches",
+            "trunks",
+            "dead leaves",
+            "live grass",
+        ]
+        colors = [
+            "darksalmon",
+            "peru",
+            "saddlebrown",
+            "black",
+            "moccasin",
+            "yellowgreen",
+        ]
+        fuel_models = [str(f) for f in fuel_dat.fuel_model.values]
+
+        if by_litter_type:
+            data_dict = {
+                lc: fuel_dat.isel(litter_class=i)[var].values
+                for i, lc in enumerate(litter_classes)
+            }
+        else:
+            data_dict = fuel_dat[var].values
+
+        _, ax = plt.subplots()
+        if by_litter_type:
+            bottom = np.zeros(len(fuel_models))
+            for i, (litter_class, dat) in enumerate(data_dict.items()):
+                ax.bar(
+                    fuel_models,
+                    dat,
+                    0.5,
+                    label=litter_class,
+                    bottom=bottom,
+                    color=colors[i],
+                )
+                bottom += dat
+            plt.legend(loc="center left", bbox_to_anchor=(1, 0.5))
+        else:
+            ax.bar(fuel_models, data_dict, color="darkcyan")
+
+        box = ax.get_position()
+        ax.set_position([box.x0, box.y0, box.width * 0.75, box.height])
+        plt.ylabel(f"{varname} ({units})", fontsize=11)
+        plt.xticks(rotation=90)
+        plt.xlabel("Fuel Model")
+
+        if save_figs:
+            fig_name = os.path.join(plot_dir, f"{varname}_plot.png")
+            plt.savefig(fig_name)
+
+    @staticmethod
+    def plot_NI_dat(fuel_dat: xr.Dataset, save_figs: bool, plot_dir: str):
+        """Plot output for Nesterov index
+
+        Args:
+            fuel_dat (Xarray Dataset): output fuel data
+            save_figs (bool): whether or not to save the figures
+            plot_dir (str): plot directory
+        """
+
+        plt.figure()
+        fuel_dat.NI.plot()
+        plt.xlabel("Time", fontsize=11)
+        plt.ylabel("Nesterov Index", fontsize=11)
+
+        if save_figs:
+            fig_name = os.path.join(plot_dir, "Nesterov_plot.png")
+            plt.savefig(fig_name)
+
+    @staticmethod
+    def plot_moisture_dat(fuel_dat: xr.Dataset, save_figs: bool, plot_dir: str):
+        """Plot output for fuel moisture
+
+        Args:
+            fuel_dat (Xarray Dataset): output fuel data
+            save_figs (bool): whether or not to save the figures
+            plot_dir (str): plot directory
+        """
+
+        plt.figure()
+        fuel_dat.fuel_moisture.plot(hue="fuel_model")
+        plt.xlabel("Time", fontsize=11)
+        plt.ylabel("Fuel Moisture", fontsize=11)
+
+        if save_figs:
+            fig_name = os.path.join(plot_dir, "fuel_moisture_plot.png")
+            plt.savefig(fig_name)

testing/functional_tests.cfg

@@ -13,4 +13,8 @@ use_param_file = False
 other_args = []
 
 [fuel]
-test_dir = fates_fuel_ftest
+test_dir = fates_fuel_ftest
+test_exe = FATES_fuel_exe
+out_file = fuel_out.nc
+use_param_file = True
+other_args = ['../testing/test_data/BONA_datm.nc']

testing/run_functional_tests.py

@@ -36,12 +36,19 @@
 
 # add testing subclasses here
 from functional_class import FunctionalTest
-from functional_testing.allometry.allometry_test import AllometryTest # pylint: disable=unused-import
-from functional_testing.math_utils.math_utils_test import QuadraticTest # pylint: disable=unused-import
+from functional_testing.allometry.allometry_test import (
+    AllometryTest,
+)  # pylint: disable=unused-import
+from functional_testing.math_utils.math_utils_test import (
+    QuadraticTest,
+)  # pylint: disable=unused-import
+from functional_testing.fire.fuel_test import FuelTest  # pylint: disable=unused-import
 
 add_cime_lib_to_path()
 
-from CIME.utils import run_cmd_no_fail  # pylint: disable=wrong-import-position,import-error,wrong-import-order
+from CIME.utils import (
+    run_cmd_no_fail,
+)  # pylint: disable=wrong-import-position,import-error,wrong-import-order
 
 # constants for this script
 _DEFAULT_CONFIG_FILE = "functional_tests.cfg"

testing/unit_tests.cfg

@@ -1,2 +1,5 @@
 [fire_weather]
 test_dir = fates_fire_weather_utest
+
+[fire_fuel]
+test_dir = fates_fire_fuel_utest