Namelist Refactor

.github/workflows/pace_tests.yaml

@@ -9,8 +9,10 @@ on:
       - main # ... when merging into the main branch
 
 jobs:
-  pace_main_tests:
-    uses: NOAA-GFDL/pace/.github/workflows/main_unit_tests.yaml@develop
+  pace_unit_tests:
+    # TODO: Revert tests back to GFDL (not jjuyeonkim) after merging
+    # https://github.com/NOAA-GFDL/NDSL/issues/64
+    uses: jjuyeonkim/pace/.github/workflows/main_unit_tests.yaml@20250908_namelist_2
     with:
       component_trigger: true
       component_name: pyFV3

.github/workflows/pyshield_tests.yaml

@@ -10,7 +10,9 @@ on:
 
 jobs:
   pyshield_translate_tests:
-    uses: NOAA-GFDL/PySHiELD/.github/workflows/translate.yaml@develop
+    # TODO: Revert tests back to GFDL (not jjuyeonkim) after merging
+    # https://github.com/NOAA-GFDL/NDSL/issues/64
+    uses: jjuyeonkim/PySHiELD/.github/workflows/translate.yaml@20250908_namelist_2
     with:
       component_trigger: true
       component_name: pyFV3

.github/workflows/translate.yaml

@@ -44,7 +44,9 @@ jobs:
         uses: actions/checkout@v5
         with:
           submodules: 'recursive'
-          repository: noaa-gfdl/pyFV3
+          # TODO: Revert tests back to GFDL (not jjuyeonkim) after merging https://github.com/NOAA-GFDL/NDSL/issues/64
+          repository: jjuyeonkim/pyFV3
+          ref: 20250908_namelist_2
           path: pyFV3
 
       - name: Checkout hash that triggered CI

pyfv3/_config.py

@@ -6,13 +6,18 @@
 import f90nml
 import yaml
 
-from ndsl.namelist import Namelist, NamelistDefaults
+from ndsl import Namelist
 
 
 DEFAULT_INT = 0
 DEFAULT_STR = ""
 DEFAULT_FLOAT = 0.0
 DEFAULT_BOOL = False
+DEFAULT_NML_GROUPS = (
+    "main_nml",
+    "coupler_nml",
+    "fv_core_nml",
+)  # TODO Double-check for any additional groups
 
 
 @dataclasses.dataclass(frozen=True)
@@ -195,86 +200,60 @@ class DynamicalCoreConfig:
     vtdm4: float = DEFAULT_FLOAT
     z_tracer: bool = DEFAULT_BOOL
     do_qa: bool = DEFAULT_BOOL
-    layout: Tuple[int, int] = NamelistDefaults.layout
-    grid_type: int = NamelistDefaults.grid_type
-    u_max: float = NamelistDefaults.u_max  # max windspeed for dp config
-    do_f3d: bool = NamelistDefaults.do_f3d
-    inline_q: bool = NamelistDefaults.inline_q
-    do_skeb: bool = NamelistDefaults.do_skeb  # save dissipation estimate
-    use_logp: bool = NamelistDefaults.use_logp
-    moist_phys: bool = NamelistDefaults.moist_phys
-    check_negative: bool = NamelistDefaults.check_negative
+    layout: Tuple[int, int] = (1, 1)
+    grid_type: int = 0
+    u_max: float = 350.0  # max windspeed for dp config
+    do_f3d: bool = False
+    inline_q: bool = False
+    do_skeb: bool = False  # save dissipation estimate
+    use_logp: bool = False
+    moist_phys: bool = True
+    check_negative: bool = False
     # gfdl_cloud_microphys.F90
-    tau_r2g: float = NamelistDefaults.tau_r2g  # rain freezing during fast_sat
-    tau_smlt: float = NamelistDefaults.tau_smlt  # snow melting
-    tau_g2r: float = NamelistDefaults.tau_g2r  # graupel melting to rain
-    tau_imlt: float = NamelistDefaults.tau_imlt  # cloud ice melting
-    tau_i2s: float = NamelistDefaults.tau_i2s  # cloud ice to snow auto - conversion
-    tau_l2r: float = NamelistDefaults.tau_l2r  # cloud water to rain auto - conversion
-    tau_g2v: float = NamelistDefaults.tau_g2v  # graupel sublimation
-    tau_v2g: float = (
-        NamelistDefaults.tau_v2g
-    )  # graupel deposition -- make it a slow process
-    sat_adj0: float = (
-        NamelistDefaults.sat_adj0
-    )  # adjustment factor (0: no 1: full) during fast_sat_adj
+    tau_r2g: float = 900.0  # rain freezing during fast_sat
+    tau_smlt: float = 900.0  # snow melting
+    tau_g2r: float = 600.0  # graupel melting to rain
+    tau_imlt: float = 600.0  # cloud ice melting
+    tau_i2s: float = 1000.0  # cloud ice to snow auto - conversion
+    tau_l2r: float = 900.0  # cloud water to rain auto - conversion
+    tau_g2v: float = 1200.0  # graupel sublimation
+    tau_v2g: float = 21600.0  # graupel deposition -- make it a slow process
+    sat_adj0: float = 0.90  # adjustment factor (0: no 1: full) during fast_sat_adj
     ql_gen: float = (
         1.0e-3  # max new cloud water during remapping step if fast_sat_adj = .t.
     )
-    ql_mlt: float = (
-        NamelistDefaults.ql_mlt
-    )  # max value of cloud water allowed from melted cloud ice
-    qs_mlt: float = NamelistDefaults.qs_mlt  # max cloud water due to snow melt
-    ql0_max: float = (
-        NamelistDefaults.ql0_max
-    )  # max cloud water value (auto converted to rain)
-    t_sub: float = NamelistDefaults.t_sub  # min temp for sublimation of cloud ice
-    qi_gen: float = (
-        NamelistDefaults.qi_gen
-    )  # max cloud ice generation during remapping step
-    qi_lim: float = (
-        NamelistDefaults.qi_lim
-    )  # cloud ice limiter to prevent large ice build up
-    qi0_max: float = NamelistDefaults.qi0_max  # max cloud ice value (by other sources)
-    rad_snow: bool = (
-        NamelistDefaults.rad_snow
-    )  # consider snow in cloud fraction calculation
-    rad_rain: bool = (
-        NamelistDefaults.rad_rain
-    )  # consider rain in cloud fraction calculation
-    rad_graupel: bool = (
-        NamelistDefaults.rad_graupel
-    )  # consider graupel in cloud fraction calculation
-    tintqs: bool = (
-        NamelistDefaults.tintqs
-    )  # use temperature in the saturation mixing in PDF
-    dw_ocean: float = NamelistDefaults.dw_ocean  # base value for ocean
-    dw_land: float = (
-        NamelistDefaults.dw_land
-    )  # base value for subgrid deviation / variability over land
+    ql_mlt: float = 2.0e-3  # max value of cloud water allowed from melted cloud ice
+    qs_mlt: float = 1.0e-6  # max cloud water due to snow melt
+    ql0_max: float = 2.0e-3  # max cloud water value (auto converted to rain)
+    t_sub: float = 184.0  # min temp for sublimation of cloud ice
+    qi_gen: float = 1.82e-6  # max cloud ice generation during remapping step
+    qi_lim: float = 1.0  # cloud ice limiter to prevent large ice build up
+    qi0_max: float = 1.0e-4  # max cloud ice value (by other sources)
+    rad_snow: bool = True  # consider snow in cloud fraction calculation
+    rad_rain: bool = True  # consider rain in cloud fraction calculation
+    rad_graupel: bool = True  # consider graupel in cloud fraction calculation
+    tintqs: bool = False  # use temperature in the saturation mixing in PDF
+    dw_ocean: float = 0.10  # base value for ocean
+    dw_land: float = 0.15  # base value for subgrid deviation / variability over land
     # cloud scheme 0 - ?
     # 1: old fvgfs gfdl) mp implementation
     # 2: binary cloud scheme (0 / 1)
-    icloud_f: int = NamelistDefaults.icloud_f
-    cld_min: float = NamelistDefaults.cld_min  # !< minimum cloud fraction
-    tau_l2v: float = (
-        NamelistDefaults.tau_l2v
-    )  # cloud water to water vapor (evaporation)
-    tau_v2l: float = (
-        NamelistDefaults.tau_v2l
-    )  # water vapor to cloud water (condensation)
-    c2l_ord: int = NamelistDefaults.c2l_ord
-    regional: bool = NamelistDefaults.regional
-    m_split: int = NamelistDefaults.m_split
-    convert_ke: bool = NamelistDefaults.convert_ke
-    breed_vortex_inline: bool = NamelistDefaults.breed_vortex_inline
-    use_old_omega: bool = NamelistDefaults.use_old_omega
-    rf_fast: bool = NamelistDefaults.rf_fast
-    adiabatic: bool = NamelistDefaults.adiabatic
-    nf_omega: int = NamelistDefaults.nf_omega
-    fv_sg_adj: int = NamelistDefaults.fv_sg_adj
-    n_sponge: int = NamelistDefaults.n_sponge
-    sw_dynamics: bool = False  # TODO: Change to NamelistDefaults.sw_dynamics
+    icloud_f: int = 0
+    cld_min: float = 0.05  # !< minimum cloud fraction
+    tau_l2v: float = 300.0  # cloud water to water vapor (evaporation)
+    tau_v2l: float = 90.0  # water vapor to cloud water (condensation)
+    c2l_ord: int = 4
+    regional: bool = False
+    m_split: int = 0
+    convert_ke: bool = False
+    breed_vortex_inline: bool = False
+    use_old_omega: bool = True
+    rf_fast: bool = False
+    adiabatic: bool = False
+    nf_omega: int = 1
+    fv_sg_adj: int = -1
+    n_sponge: int = 1
+    sw_dynamics: bool = False  # shallow water conditions
     namelist_override: Optional[str] = None
 
     def __post_init__(self):
@@ -291,125 +270,65 @@ def __post_init__(self):
         if self.grid_type > 3:
             self.nf_omega = 0
 
+    # TODO: Consider removing from_namelist or from_f90nml. Duplicates.
     @classmethod
-    def from_f90nml(cls, f90_namelist: f90nml.Namelist) -> "DynamicalCoreConfig":
-        namelist = Namelist.from_f90nml(f90_namelist)
-        return cls.from_namelist(namelist)
+    def from_namelist(
+        cls, namelist: Namelist, target_groups=None
+    ) -> "DynamicalCoreConfig":
+        """This creates a DynamicalCoreConfig using the input namelist.
+        Duplicate of from_f90nml.
+        """
+        return cls.from_f90nml(namelist, target_groups=target_groups)
 
     @classmethod
-    def from_namelist(cls, namelist: Namelist) -> "DynamicalCoreConfig":
-        return cls(
-            dt_atmos=namelist.dt_atmos,
-            a_imp=namelist.a_imp,
-            beta=namelist.beta,
-            consv_te=namelist.consv_te,
-            d2_bg=namelist.d2_bg,
-            d2_bg_k1=namelist.d2_bg_k1,
-            d2_bg_k2=namelist.d2_bg_k2,
-            d4_bg=namelist.d4_bg,
-            d_con=namelist.d_con,
-            d_ext=namelist.d_ext,
-            dddmp=namelist.dddmp,
-            delt_max=namelist.delt_max,
-            do_sat_adj=namelist.do_sat_adj,
-            do_vort_damp=namelist.do_vort_damp,
-            fill=namelist.fill,
-            hord_dp=namelist.hord_dp,
-            hord_mt=namelist.hord_mt,
-            hord_tm=namelist.hord_tm,
-            hord_tr=namelist.hord_tr,
-            hord_vt=namelist.hord_vt,
-            hydrostatic=namelist.hydrostatic,
-            k_split=namelist.k_split,
-            ke_bg=namelist.ke_bg,
-            kord_mt=namelist.kord_mt,
-            kord_tm=namelist.kord_tm,
-            kord_tr=namelist.kord_tr,
-            kord_wz=namelist.kord_wz,
-            n_split=namelist.n_split,
-            nord=namelist.nord,
-            npx=namelist.npx,
-            npy=namelist.npy,
-            npz=namelist.npz,
-            ntiles=namelist.ntiles,
-            nwat=namelist.nwat,
-            p_fac=namelist.p_fac,
-            rf_cutoff=namelist.rf_cutoff,
-            tau=namelist.tau,
-            vtdm4=namelist.vtdm4,
-            z_tracer=namelist.z_tracer,
-            do_qa=namelist.do_qa,
-            layout=namelist.layout,
-            grid_type=namelist.grid_type,
-            u_max=namelist.u_max,
-            do_f3d=namelist.do_f3d,
-            inline_q=namelist.inline_q,
-            do_skeb=namelist.do_skeb,
-            check_negative=namelist.check_negative,
-            tau_r2g=namelist.tau_r2g,
-            tau_smlt=namelist.tau_smlt,
-            tau_g2r=namelist.tau_g2r,
-            tau_imlt=namelist.tau_imlt,
-            tau_i2s=namelist.tau_i2s,
-            tau_l2r=namelist.tau_l2r,
-            tau_g2v=namelist.tau_g2v,
-            tau_v2g=namelist.tau_v2g,
-            sat_adj0=namelist.sat_adj0,
-            ql_gen=namelist.ql_gen,
-            ql_mlt=namelist.ql_mlt,
-            qs_mlt=namelist.qs_mlt,
-            ql0_max=namelist.ql0_max,
-            t_sub=namelist.t_sub,
-            qi_gen=namelist.qi_gen,
-            qi_lim=namelist.qi_lim,
-            qi0_max=namelist.qi0_max,
-            rad_snow=namelist.rad_snow,
-            rad_rain=namelist.rad_rain,
-            rad_graupel=namelist.rad_graupel,
-            tintqs=namelist.tintqs,
-            dw_ocean=namelist.dw_ocean,
-            dw_land=namelist.dw_land,
-            icloud_f=namelist.icloud_f,
-            cld_min=namelist.cld_min,
-            tau_l2v=namelist.tau_l2v,
-            tau_v2l=namelist.tau_v2l,
-            c2l_ord=namelist.c2l_ord,
-            regional=namelist.regional,
-            m_split=namelist.m_split,
-            convert_ke=namelist.convert_ke,
-            breed_vortex_inline=namelist.breed_vortex_inline,
-            use_old_omega=namelist.use_old_omega,
-            rf_fast=namelist.rf_fast,
-            adiabatic=namelist.adiabatic,
-            nf_omega=namelist.nf_omega,
-            fv_sg_adj=namelist.fv_sg_adj,
-            n_sponge=namelist.n_sponge,
-        )
+    def from_f90nml(
+        cls, namelist: f90nml.Namelist, target_groups=None
+    ) -> "DynamicalCoreConfig":
+        """This creates a DynamicalCoreConfig using the input namelist.
+        Args:
+            namelist
+            target_groups - If None, then the DEFAULT_NML_GROUPS will be used to populate the dataclass fields.
+        """
+        namelist = Namelist(namelist)
+        if target_groups is None:
+            groups = DEFAULT_NML_GROUPS
+        else:
+            groups = target_groups
+
+        namelist_dict = namelist.namelist_groups_to_flatish_dict(groups)
+        namelist_dict = {
+            key: value
+            for key, value in namelist_dict.items()
+            if key in cls.__dataclass_fields__  # type: ignore
+        }
+        return cls(**namelist_dict)
 
     @classmethod
-    def from_yaml(cls, yaml_config: str) -> "DynamicalCoreConfig":
+    def from_yaml_dict(cls, yaml_dict: dict) -> "DynamicalCoreConfig":
+        """TOODO
+        Args:
+            yaml_dict: dict, as if read from yaml safe_load
+        """
         config = cls()
-        with open(yaml_config, "r") as f:
-            raw_config = yaml.safe_load(f)
         flat_config: dict = {}
-        timestep = timedelta(seconds=raw_config["dt_atmos"])
+        timestep = timedelta(seconds=yaml_dict["dt_atmos"])
         runtime = {
             "days": 0.0,
             "hours": 0.0,
             "minutes": 0.0,
             "seconds": 0.0,
         }
         for key in runtime.keys():
-            if key in raw_config.keys():
-                runtime[key] = raw_config[key]
+            if key in yaml_dict.keys():
+                runtime[key] = yaml_dict[key]
 
         total_time = timedelta(
             days=runtime["days"],
             hours=runtime["hours"],
             minutes=runtime["minutes"],
             seconds=runtime["seconds"],
         )
-        for key, value in raw_config.items():
+        for key, value in yaml_dict.items():
             if isinstance(value, dict):
                 for subkey, subvalue in value.items():
                     if subkey in config.__annotations__.keys():
@@ -435,6 +354,12 @@ def from_yaml(cls, yaml_config: str) -> "DynamicalCoreConfig":
         config.n_steps = floor(total_time.total_seconds() / timestep.total_seconds())
         return config
 
+    @classmethod
+    def from_yaml(cls, yaml_config: str) -> "DynamicalCoreConfig":
+        with open(yaml_config, "r") as f:
+            raw_config = yaml.safe_load(f)
+        return cls.from_yaml_dict(raw_config)
+
     @property
     def do_dry_convective_adjustment(self) -> bool:
         return self.fv_sg_adj > 0

pyfv3/testing/translate_fvdynamics.py

@@ -30,7 +30,7 @@ def __init__(
         stencil_factory: StencilFactory,
     ):
         super().__init__(grid, stencil_factory)
-        self.namelist = DynamicalCoreConfig.from_namelist(namelist)
+        self.config = DynamicalCoreConfig.from_f90nml(namelist)
 
 
 class TranslateFVDynamics(ParallelTranslateBaseSlicing):

pyfv3/wrappers/geos_wrapper.py

@@ -115,8 +115,19 @@ def __init__(
         self.perf_collector = PerformanceCollector("GEOS wrapper", comm)
 
         self.backend = backend
+
+        # TODO: The namelist argument is expected to contain a hierarchy
+        # consistent with what pace expects from a yaml configuration file
+        # (rather than an input.nml configuration file).
+        # The test_geos_wrapper in test_init_from_geos.py takes that yaml
+        # hierarchy and uses it to initialize a f90nml.Namelist.
+        # This seems a bit confusing. Because of this, the dycore_config
+        # is being initialized using "from_yaml_dict", even though it's
+        # it uses a "namelist". This should eventually be cleared up, but I'm
+        # leaving it as is because I'm not sure if it's important elsewhere.
         self.namelist = namelist
-        self.dycore_config = pyfv3.DynamicalCoreConfig.from_f90nml(self.namelist)
+        self.dycore_config = pyfv3.DynamicalCoreConfig.from_yaml_dict(self.namelist)
+
         self.dycore_config.dt_atmos = bdt
         assert self.dycore_config.dt_atmos != 0