Merge branch 'main' into osf-optim

src/proteus/atmos_clim/dummy.py

@@ -33,10 +33,6 @@ def RunDummyAtm( dirs:dict, config:Config, T_magma:float, F_ins:float, R_int:flo
     skin_d          = config.atmos_clim.surface_d
     skin_k          = config.atmos_clim.surface_k
 
-    # Check configuration
-    if config.atmos_clim.rayleigh:
-        log.warning("Rayleigh scattering is enabled but it will be neglected")
-
     log.info("Gamma = %.4f" % gamma)
     if not (0.0 <= gamma <= 1.0):
         log.warning("Gamma value is out of bounds; expect unreasonable fluxes")

src/proteus/config/_atmos_clim.py

@@ -1,15 +1,25 @@
 from __future__ import annotations
 
+import logging
+
 from attrs import define, field
 from attrs.validators import ge, gt, in_, le
 
 from ._converters import none_if_none
 
+log = logging.getLogger('fwl.' + __name__)
+
 
 def tmp_max_bigger_than_tmp_min(instance, attribute, value):
     if value <= instance.tmp_minimum:
         raise ValueError("'tmp_maximum' has to be bigger than 'tmp_minimum'.")
 
+
+def warn_if_dummy(instance, attribute, value):
+    if instance.module == 'dummy':
+        log.warning('Rayleigh scattering is enabled but it will be neglected')
+
+
 @define
 class AtmosClim:
     """Atmosphere parameters, model selection.
@@ -47,6 +57,7 @@ class AtmosClim:
     dummy: Dummy
         Config parameters for dummy atmosphere module
     """
+
     prevent_warming: bool
     surface_d: float = field(validator=gt(0))
     surface_k: float = field(validator=gt(0))
@@ -55,7 +66,7 @@ class AtmosClim:
     surf_state: str = field(validator=in_(('mixed_layer', 'fixed', 'skin')))
     surf_albedo: float = field(validator=(ge(0), le(1)))
     albedo_pl: float = field(validator=(ge(0), le(1)))
-    rayleigh: bool
+    rayleigh: bool = field(validator=warn_if_dummy)
     tmp_minimum: float = field(validator=gt(0))
     tmp_maximum: float = field(validator=tmp_max_bigger_than_tmp_min)
 
@@ -88,13 +99,12 @@ class Agni:
     chemistry: str | None
         Treatment of self-consistent atmospheric chemsitry. Choices: "none", "eq", "kin".
     """
+
     p_top: float = field(validator=gt(0))
     spectral_group: str
     spectral_bands: str
     num_levels: int = field(validator=ge(15))
-    chemistry: str | None = field(
-        validator=in_((None, 'eq', 'kin')), converter=none_if_none
-    )
+    chemistry: str | None = field(validator=in_((None, 'eq', 'kin')), converter=none_if_none)
 
     @property
     def chemistry_int(self) -> int:
@@ -121,6 +131,7 @@ class Janus:
     tropopause: str | None
         Scheme for determining tropopause location. Choices: "none", "skin", "dynamic".
     """
+
     p_top: float = field(validator=gt(0))
     spectral_group: str
     spectral_bands: str
@@ -140,4 +151,5 @@ class Dummy:
     gamma: float
         Atmosphere opacity between 0 and 1.
     """
+
     gamma: float

src/proteus/config/_delivery.py

@@ -59,6 +59,10 @@ class Volatiles:
     CH4: float = field(default=0, validator=ge(0))
     CO: float = field(default=0, validator=ge(0))
 
+    def get_pressure(self, s: str) -> float:
+        """Helper method for getting the pressure for `vol` by string."""
+        return getattr(self, s)
+
 
 @define
 class Delivery:

src/proteus/config/_outgas.py

@@ -32,6 +32,8 @@ class Calliope:
 
     Attributes
     ----------
+    T_floor: float
+        Temperature floor applied to outgassing calculation [K].
     include_H2O: bool
         If True, include H2O outgassing.
     include_CO2: bool
@@ -48,18 +50,20 @@ class Calliope:
         If True, include CH4 outgassing.
     include_CO: bool
         If True, include CO outgassing.
-    T_floor: float
-        Temperature floor applied to outgassing calculation [K].
     """
-    include_H2O: bool
-    include_CO2: bool
-    include_N2: bool
-    include_S2: bool
-    include_SO2: bool
-    include_H2: bool
-    include_CH4: bool
-    include_CO: bool
     T_floor: float  = field(validator=validators.gt(0.0))
+    include_H2O: bool = False
+    include_CO2: bool = False
+    include_N2: bool = False
+    include_S2: bool = False
+    include_SO2: bool = False
+    include_H2: bool = False
+    include_CH4: bool = False
+    include_CO: bool = False
+
+    def is_included(self, vol: str) -> bool:
+        """Helper method for getting flag if `vol` is included in outgassing."""
+        return getattr(self, f'include_{vol}')
 
 
 @define

src/proteus/outgas/calliope.py

@@ -43,12 +43,12 @@ def construct_options(dirs:dict, config:Config, hf_row:dict):
 
     # Volatile inventory
     for s in vol_list:
-        solvevol_inp[f'{s}_initial_bar'] =  getattr(config.delivery.volatiles, s)
+        solvevol_inp[f'{s}_initial_bar'] = config.delivery.volatiles.get_pressure(s)
 
-        included = getattr(config.outgas.calliope, f'include_{s}')
-        solvevol_inp[f'{s}_included'] = 1 if included else 0
+        included = config.outgas.calliope.is_included(s)
+        solvevol_inp[f'{s}_included'] = int(included)
 
-        if (s in ["H2O","CO2","N2","S2"]) and not included:
+        if (s in ("H2O","CO2","N2","S2")) and not included:
             UpdateStatusfile(dirs, 20)
             raise RuntimeError(f"Missing required volatile {s}")
 

src/proteus/plot/cpl_fluxes_global.py

@@ -13,10 +13,11 @@
 
 if TYPE_CHECKING:
     from proteus import Proteus
+    from proteus.config import Config
 
 log = logging.getLogger("fwl."+__name__)
 
-def plot_fluxes_global(hf_all:pd.DataFrame, output_dir: str, options: dict, t0: float=100.0):
+def plot_fluxes_global(hf_all:pd.DataFrame, output_dir: str, config: Config, t0: float=100.0):
 
     # Get values
     hf_crop = hf_all.loc[hf_all["Time"]>t0]
@@ -28,7 +29,7 @@ def plot_fluxes_global(hf_all:pd.DataFrame, output_dir: str, options: dict, t0:
     log.info("Plot global fluxes")
 
     F_net = np.array(hf_crop["F_atm"])
-    F_asf = np.array(hf_crop["F_ins"]) * options["asf_scalefactor"] * (1.0 - options["albedo_pl"]) * np.cos(options["zenith_angle"] * np.pi/180.0)
+    F_asf = np.array(hf_crop["F_ins"]) * config.orbit.s0_factor * (1.0 - config.atmos_clim.albedo_pl) * np.cos(config.orbit.zenith_angle * np.pi/180.0)
     F_olr = np.array(hf_crop["F_olr"])
     F_upw = np.array(hf_crop["F_olr"]) + np.array(hf_crop["F_sct"])
     F_int = np.array(hf_crop["F_int"])
@@ -63,7 +64,7 @@ def plot_fluxes_global(hf_all:pd.DataFrame, output_dir: str, options: dict, t0:
 
     plt.close()
     plt.ioff()
-    fig.savefig(output_dir+"/plot_fluxes_global.%s"%options["plot_format"],
+    fig.savefig(output_dir+"/plot_fluxes_global.%s" % config.params.out.plot_fmt,
                 bbox_inches='tight', dpi=200)
 
 
@@ -75,7 +76,7 @@ def plot_fluxes_global_entry(handler: Proteus):
     plot_fluxes_global(
         hf_all=hf_all,
         output_dir=handler.directories["output"],
-        options=handler.config,
+        config=handler.config,
     )
 
 

src/proteus/plot/cpl_global.py

@@ -14,10 +14,11 @@
 
 if TYPE_CHECKING:
     from proteus import Proteus
+    from proteus.config import Config
 
 log = logging.getLogger("fwl."+__name__)
 
-def plot_global(hf_all: pd.DataFrame, output_dir: str, options: dict,
+def plot_global(hf_all: pd.DataFrame, output_dir: str, config: Config,
                 logt: bool=True, tmin: float=1e1):
 
     if np.amax(hf_all["Time"]) < 2:
@@ -51,7 +52,8 @@ def plot_global(hf_all: pd.DataFrame, output_dir: str, options: dict,
         # Check vmr for presence
         this_vmr = np.array(hf_all[vol+"_vmr"])
         vol_present[vol] = True
-        if (np.amax(this_vmr) < 1.0e-20) or (options[vol+"_included"] < 1):
+
+        if (np.amax(this_vmr) < 1.0e-20) or not config.outgas.calliope.is_included(vol):
             vol_present[vol] = False
             continue
         vol_vmr[vol] = this_vmr
@@ -154,9 +156,10 @@ def plot_global(hf_all: pd.DataFrame, output_dir: str, options: dict,
     ax_cl.set_ylim(min(1000.0,min_temp-25) , max(3500.0,max_temp+25))
 
     # PLOT ax_bl
-    ax_bl.axhline( y=options["planet_coresize"], ls='dashed', lw=lw*1.5, alpha=al, color=get_colour("core"), label=r'C-M boundary' )
+    ax_bl.axhline( y=config.struct.corefrac,     ls='dashed', lw=lw*1.5, alpha=al, color=get_colour("core"), label=r'C-M boundary' )
     ax_bl.plot( hf_all["Time"], 1.0-hf_all["RF_depth"],   color=get_colour("int"), ls="solid",    lw=lw, alpha=al, label=r'Rheol. front')
     ax_bl.plot( hf_all["Time"],     hf_all["Phi_global"], color=get_colour("atm"), linestyle=':', lw=lw, alpha=al, label=r'Melt fraction')
+
     ax_bl.legend(loc='center left', **leg_kwargs)
     ax_bl.set_ylim(0.0,1.01)
 
@@ -195,7 +198,7 @@ def plot_global(hf_all: pd.DataFrame, output_dir: str, options: dict,
     else:
         plt_name += "_lin"
 
-    fig.savefig(output_dir+"/%s.%s"%(plt_name,options["plot_format"]),
+    fig.savefig(output_dir+"/%s.%s"%(plt_name,config.params.out.plot_fmt),
                 bbox_inches='tight', dpi=200)
 
 
@@ -208,7 +211,7 @@ def plot_global_entry(handler: Proteus):
         plot_global(
             hf_all=hf_all,
             output_dir=handler.directories['output'],
-            options=handler.config,
+            config=handler.config,
             logt=logt,
             tmin=1e1,
         )

src/proteus/proteus.py

@@ -192,8 +192,8 @@ def start(self, *, resume: bool = False):
             log.info("Input partial pressures:")
             inc_gases = []
             for s in vol_list:
-                pp_val = getattr(self.config.delivery.volatiles, s)
-                include = getattr(self.config.outgas.calliope, f'include_{s}')
+                pp_val = self.config.delivery.volatiles.get_pressure(s)
+                include = self.config.outgas.calliope.is_included(s)
 
                 log.info(
                     "    %-6s : %-5.2f bar (included = %s)"

src/proteus/star/wrapper.py

@@ -140,8 +140,10 @@ def get_new_spectrum(t_star:float, config:Config,
         match config.star.mors.tracks:
             case 'spada':
                 star_props_hist = get_spada_synthesis_properties(stellar_track, t_star/1e6)
+                assert star_struct_modern
+                assert star_props_modern
                 synthetic = mors.synthesis.CalcScaledSpectrumFromProps(
-                    star_struct_modern, star_props_modern, star_props_hist)
+                    modern_spec=star_struct_modern, modern_dict=star_props_modern, historical_dict=star_props_hist)
                 fl = synthetic.fl
                 wl = synthetic.wl
             case 'baraffe':

tests/test_config.py

@@ -8,6 +8,8 @@
 from proteus import Proteus
 from proteus.config import Config, read_config_object
 from proteus.config._converters import none_if_none
+from proteus.config._delivery import Volatiles
+from proteus.config._outgas import Calliope
 
 PATHS = chain(
     (PROTEUS_ROOT / 'input').glob('*.toml'),
@@ -50,3 +52,24 @@ def test_proteus_init(path):
     runner = Proteus(config_path=path)
 
     assert isinstance(runner.config, Config)
+
+
+def test_calliope_is_included():
+    conf = Calliope(
+        T_floor=0.1,
+        include_CO=False,
+        include_H2=True,
+    )
+    assert not conf.is_included('CO')
+    assert conf.is_included('H2')
+    with pytest.raises(AttributeError):
+        conf.is_included('fails')
+
+
+def test_delivery_get_pressure():
+    conf = Volatiles(
+        N2 = 123.0
+    )
+    assert conf.get_pressure('N2') == 123.0
+    with pytest.raises(AttributeError):
+        conf.get_pressure('fails')