Restructure radiation field

docs/physics/update_and_conv/update_and_conv.ipynb

@@ -191,15 +191,15 @@
     "\n",
     "# We manually put in the damping constants and t_inner_update_exponent for\n",
     "# illustrative purposes:\n",
-    "d_t_rad = 0.5\n",
-    "d_w = 0.3\n",
-    "d_t_inner = 0.7\n",
+    "damping_t_radiative = 0.5\n",
+    "damping_dilution_factor = 0.3\n",
+    "damping_t_inner = 0.7\n",
     "t_inner_update_exponent = -0.5\n",
     "\n",
     "# We set the above values into the configuration:\n",
-    "tardis_config.montecarlo.convergence_strategy.t_rad.damping_constant = d_t_rad\n",
-    "tardis_config.montecarlo.convergence_strategy.w.damping_constant = d_w\n",
-    "tardis_config.montecarlo.convergence_strategy.t_inner.damping_constant = d_t_inner\n",
+    "tardis_config.montecarlo.convergence_strategy.t_rad.damping_constant = damping_t_radiative\n",
+    "tardis_config.montecarlo.convergence_strategy.w.damping_constant = damping_dilution_factor\n",
+    "tardis_config.montecarlo.convergence_strategy.t_inner.damping_constant = damping_t_inner\n",
     "tardis_config.montecarlo.convergence_strategy.t_inner_update_exponent = t_inner_update_exponent"
    ]
   },
@@ -212,7 +212,7 @@
    "source": [
     "sim = Simulation.from_config(tardis_config)\n",
     "\n",
-    "model = sim.simulation_state\n",
+    "simulation_state = sim.simulation_state\n",
     "plasma = sim.plasma\n",
     "transport = sim.transport"
    ]
@@ -233,7 +233,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "model.t_rad"
+    "simulation_state.t_radiative"
    ]
   },
   {
@@ -243,7 +243,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "model.w"
+    "simulation_state.dilution_factor"
    ]
   },
   {
@@ -253,7 +253,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "model.t_inner"
+    "simulation_state.t_inner"
    ]
   },
   {
@@ -344,8 +344,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "V = model.volume\n",
-    "Delta_t = transport.calculate_time_of_simulation(model)\n",
+    "V = simulation_state.volume\n",
+    "Delta_t = transport.calculate_time_of_simulation(simulation_state)\n",
     "prefactor = 1 / (4 * np.pi * V * Delta_t)\n",
     "J = prefactor * j_estimator\n",
     "J"
@@ -410,7 +410,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "t_rad_updated = model.t_rad + d_t_rad * (t_rad_estimated - model.t_rad)\n",
+    "t_rad_updated = simulation_state.t_radiative + damping_t_radiative * (t_rad_estimated - simulation_state.t_radiative)\n",
     "t_rad_updated"
    ]
   },
@@ -421,8 +421,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "w_estimated = ( j_estimator / (4 * const.sigma_sb.cgs * t_rad_estimated**4 * V * Delta_t) ).decompose()\n",
-    "w_estimated"
+    "dilution_factor_estimated = ( j_estimator / (4 * const.sigma_sb.cgs * t_rad_estimated**4 * V * Delta_t) ).decompose()\n",
+    "dilution_factor_estimated"
    ]
   },
   {
@@ -432,8 +432,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "w_updated = model.w + d_w * (w_estimated - model.w)\n",
-    "w_updated"
+    "dilution_factor_updated = simulation_state.dilution_factor + damping_dilution_factor * (dilution_factor_estimated - simulation_state.dilution_factor)\n",
+    "dilution_factor_updated"
    ]
   },
   {
@@ -484,7 +484,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "t_inner_estimated = model.t_inner * (L_output / L_requested)**t_inner_update_exponent\n",
+    "t_inner_estimated = simulation_state.t_inner * (L_output / L_requested)**t_inner_update_exponent\n",
     "t_inner_estimated"
    ]
   },
@@ -495,7 +495,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "t_inner_updated = model.t_inner + d_t_inner * (t_inner_estimated - model.t_inner)\n",
+    "t_inner_updated = simulation_state.t_inner + damping_t_inner * (t_inner_estimated - simulation_state.t_inner)\n",
     "t_inner_updated"
    ]
   },
@@ -536,7 +536,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "model.t_rad"
+    "simulation_state.t_radiative"
    ]
   },
   {
@@ -548,7 +548,7 @@
    },
    "outputs": [],
    "source": [
-    "model.w"
+    "simulation_state.dilution_factor"
    ]
   },
   {
@@ -558,7 +558,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "model.t_inner"
+    "simulation_state.t_inner"
    ]
   },
   {

tardis/io/model/model_reader.py

@@ -282,7 +282,7 @@ def transport_from_hdf(fname):
     return new_transport
 
 
-def simulation_state_to_dict(model):
+def simulation_state_to_dict(simulation_state):
     """
     Retrieves all the data from a SimulationState object and returns a dictionary.
 
@@ -296,20 +296,20 @@ def simulation_state_to_dict(model):
     isotope_abundance : dict
     """
     simulation_state_dict = {
-        "velocity_cgs": model.velocity.cgs,
-        "abundance": model.abundance,
-        "time_explosion_cgs": model.time_explosion.cgs,
-        "t_inner_cgs": model.t_inner.cgs,
-        "t_radiative_cgs": model.t_radiative.cgs,
-        "dilution_factor": model.dilution_factor,
-        "v_boundary_inner_cgs": model.v_boundary_inner.cgs,
-        "v_boundary_outer_cgs": model.v_boundary_outer.cgs,
-        "w": model.w,
-        "t_rad_cgs": model.t_rad.cgs,
-        "r_inner_cgs": model.r_inner.cgs,
-        "density_cgs": model.density.cgs,
+        "velocity_cgs": simulation_state.velocity.cgs,
+        "abundance": simulation_state.abundance,
+        "time_explosion_cgs": simulation_state.time_explosion.cgs,
+        "t_inner_cgs": simulation_state.t_inner.cgs,
+        "t_radiative_cgs": simulation_state.t_radiative.cgs,
+        "dilution_factor": simulation_state.dilution_factor,
+        "v_boundary_inner_cgs": simulation_state.v_boundary_inner.cgs,
+        "v_boundary_outer_cgs": simulation_state.v_boundary_outer.cgs,
+        "dilution_factor": simulation_state.dilution_factor,
+        "r_inner_cgs": simulation_state.r_inner.cgs,
+        "density_cgs": simulation_state.density.cgs,
     }
 
+    for key, value in simulation_state_dict.items():
     for key, value in simulation_state_dict.items():
         if hasattr(value, "unit"):
             simulation_state_dict[key] = [
@@ -318,75 +318,3 @@ def simulation_state_to_dict(model):
             ]
 
     return simulation_state_dict
-
-
-def model_from_hdf(fname):
-    """
-    Creates a SimulationState object using data stored in a hdf file.
-
-    Parameters
-    ----------
-    fname : str
-
-    Returns
-    -------
-    new_model : tardis.model.SimulationState
-    """
-
-    from tardis.model import SimulationState
-
-    d = {}
-
-    # Loading data from hdf file
-    with h5py.File(fname, "r") as f:
-        model_group = f["model"]
-        for key, value in model_group.items():
-            if not key.endswith("_unit"):
-                if type(value) == h5py._hl.dataset.Dataset:
-                    if isinstance(value[()], bytes):
-                        d[key] = value[()].decode("utf-8")
-                    else:
-                        d[key] = value[()]
-                else:
-                    data_inner = {}
-                    for key_inner, value_inner in value.items():
-                        if isinstance(value_inner[()], bytes):
-                            data_inner[key] = value_inner[()].decode("utf-8")
-                        else:
-                            data_inner[key] = value_inner[()]
-                        data_inner[key_inner] = value_inner[()]
-                    d[key] = data_inner
-
-        for key, value in model_group.items():
-            if key.endswith("_unit"):
-                d[key[:-5]] = [d[key[:-5]], value[()]]
-
-    # Converting cgs data to astropy quantities
-    for key, value in d.items():
-        if key.endswith("_cgs"):
-            d[key] = u.Quantity(value[0], unit=u.Unit(value[1].decode("utf-8")))
-
-    homologous_density = calculate_density_after_time(
-        d["homologous_density"]["density_0"],
-        d["homologous_density"]["time_0"],
-        d["time_explosion_cgs"],
-    )
-
-    new_model = SimulationState(
-        velocity=d["velocity_cgs"],
-        density=homologous_density,
-        abundance=d["abundance"],
-        isotope_abundance=None,
-        time_explosion=d["time_explosion_cgs"],
-        elemental_mass=None,
-        t_inner=d["t_inner_cgs"],
-        t_radiative=d["t_radiative_cgs"],
-        dilution_factor=d["dilution_factor"],
-        v_boundary_inner=d["v_boundary_inner_cgs"],
-        v_boundary_outer=d["v_boundary_outer_cgs"],
-    )
-
-    new_model.t_rad = d["t_rad_cgs"]
-    new_model.w = d["w"]
-
-    return new_model

tardis/io/model_reader.py

@@ -866,72 +866,3 @@ def store_model_to_hdf(model, fname):
                 model_group.create_dataset(key + "_unit", data=value[1])
             else:
                 model_group.create_dataset(key, data=value)
-
-
-def model_from_hdf(fname):
-    """
-    Creates a SimulationState object using data stored in a hdf file.
-
-    Parameters
-    ----------
-    fname : str
-
-    Returns
-    -------
-    new_model : tardis.model.SimulationState
-    """
-
-    from tardis.model import SimulationState
-
-    d = {}
-
-    # Loading data from hdf file
-    with h5py.File(fname, "r") as f:
-        model_group = f["model"]
-        for key, value in model_group.items():
-            if not key.endswith("_unit"):
-                if type(value) == h5py._hl.dataset.Dataset:
-                    if isinstance(value[()], bytes):
-                        d[key] = value[()].decode("utf-8")
-                    else:
-                        d[key] = value[()]
-                else:
-                    data_inner = {}
-                    for key_inner, value_inner in value.items():
-                        if isinstance(value_inner[()], bytes):
-                            data_inner[key] = value_inner[()].decode("utf-8")
-                        else:
-                            data_inner[key] = value_inner[()]
-                        data_inner[key_inner] = value_inner[()]
-                    d[key] = data_inner
-
-        for key, value in model_group.items():
-            if key.endswith("_unit"):
-                d[key[:-5]] = [d[key[:-5]], value[()]]
-
-    # Converting cgs data to astropy quantities
-    for key, value in d.items():
-        if key.endswith("_cgs"):
-            d[key] = u.Quantity(value[0], unit=u.Unit(value[1].decode("utf-8")))
-
-    homologous_density = HomologousDensity(
-        d["homologous_density"]["density_0"], d["homologous_density"]["time_0"]
-    )
-
-    new_model = SimulationState(
-        velocity=d["velocity_cgs"],
-        homologous_density=homologous_density,
-        abundance=d["abundance"],
-        isotope_abundance=None,
-        time_explosion=d["time_explosion_cgs"],
-        t_inner=d["t_inner_cgs"],
-        t_radiative=d["t_radiative_cgs"],
-        dilution_factor=d["dilution_factor"],
-        v_boundary_inner=d["v_boundary_inner_cgs"],
-        v_boundary_outer=d["v_boundary_outer_cgs"],
-    )
-
-    new_model.t_rad = d["t_rad_cgs"]
-    new_model.w = d["w"]
-
-    return new_model