Revert "Restructure: Add radiation field (tardis-sn#123)" (tardis-sn#133

)

This reverts commit 1320de3.

benchmarks/run_stardis.py

@@ -11,9 +11,9 @@
 
 from stardis.io.model.marcs import read_marcs_model
 from stardis.plasma import create_stellar_plasma
-from stardis.radiation_field.opacities.opacities_solvers import calc_alphas
-from stardis.radiation_field.radiation_field_solvers import raytrace
-from stardis.radiation_field.opacities.opacities_solvers import calc_alpha_line_at_nu
+from stardis.opacities import calc_alphas
+from stardis.transport import raytrace
+from stardis.opacities import calc_alpha_line_at_nu
 
 
 class BenchmarkStardis:

stardis/base.py

@@ -9,9 +9,8 @@
 from astropy import units as u
 
 from stardis.plasma import create_stellar_plasma
-from stardis.radiation_field.opacities.opacities_solvers import calc_alphas
-from stardis.radiation_field.radiation_field_solvers import raytrace
-from stardis.radiation_field import RadiationField
+from stardis.opacities import calc_alphas
+from stardis.transport import raytrace
 
 
 base_dir = os.path.abspath(os.path.dirname(__file__))
@@ -73,34 +72,20 @@ def run_stardis(config_fname, tracing_lambdas_or_nus):
     # plasma
     stellar_plasma = create_stellar_plasma(stellar_model, adata)
 
-    if True:  # change to checking source function from config
-        from stardis.radiation_field.source_functions.blackbody import (
-            blackbody_flux_at_nu,
-        )
-
-        stellar_radiation_field = RadiationField(
-            tracing_nus, blackbody_flux_at_nu, stellar_model
-        )
-
-    calc_alphas(
+    # Below becomes radiation field
+    alphas, gammas, doppler_widths = calc_alphas(
         stellar_plasma=stellar_plasma,
         stellar_model=stellar_model,
-        stellar_radiation_field=stellar_radiation_field,
+        tracing_nus=tracing_nus,
         opacity_config=config.opacity,
     )
 
-    raytrace(stellar_model, stellar_radiation_field, no_of_thetas=config.no_of_thetas)
+    F_nu = raytrace(
+        stellar_model, alphas, tracing_nus, no_of_thetas=config.no_of_thetas
+    )
 
     return STARDISOutput(
-        stellar_plasma,
-        stellar_model,
-        stellar_radiation_field.opacities.opacities_dict,
-        stellar_radiation_field.opacities.opacities_dict["alpha_line_at_nu_gammas"],
-        stellar_radiation_field.opacities.opacities_dict[
-            "alpha_line_at_nu_doppler_widths"
-        ],
-        stellar_radiation_field.F_nu,
-        stellar_radiation_field.frequencies,
+        stellar_plasma, stellar_model, alphas, gammas, doppler_widths, F_nu, tracing_nus
     )
 
 
@@ -149,9 +134,6 @@ class STARDISOutput:
         Numpy array of wavelengths used for spectrum with units of Angstroms.
     """
 
-    ###TODO: Instead of returning all these various quantities of the radiation, simply return
-    # the radiation field with class properties that return useful quantities such as spectrum lambda and lambdas.
-
     def __init__(
         self, stellar_plasma, stellar_model, alphas, gammas, doppler_widths, F_nu, nus
     ):

stardis/opacities/__init__.py

@@ -0,0 +1 @@
+from stardis.opacities.base import *

stardis/radiation_field/opacities/opacities_solvers/base.py → stardis/opacities/base.py

@@ -3,19 +3,15 @@
 
 import numba
 
+from tardis.io.config_reader import ConfigurationNameSpace
+
 from astropy import units as u, constants as const
 
-from stardis.radiation_field.opacities.opacities_solvers.broadening import (
-    calculate_broadening,
-)
-from stardis.radiation_field.opacities.opacities_solvers.voigt import voigt_profile
-from stardis.radiation_field.opacities.opacities_solvers.util import (
-    sigma_file,
-    map_items_to_indices,
-    get_number_density,
-)
-
-# constants
+from stardis.opacities.broadening import calculate_broadening
+from stardis.opacities.voigt import voigt_profile
+from stardis.opacities.util import sigma_file, map_items_to_indices, get_number_density
+
+
 VACUUM_ELECTRIC_PERMITTIVITY = 1 / (4 * np.pi)
 BF_CONSTANT = (
     64
@@ -532,18 +528,18 @@ def calc_alan_entries(
 def calc_alphas(
     stellar_plasma,
     stellar_model,
-    stellar_radiation_field,
+    tracing_nus,
     opacity_config,
 ):
     """
-    Calculates each opacity and adds it to the opacity dictionary contained in the radiation field.
+    Calculates total opacity.
 
     Parameters
     ----------
     stellar_plasma : tardis.plasma.base.BasePlasma
     stellar_model : stardis.model.base.StellarModel
-    stellar_radiation_field stardis.radiation_field.base.RadiationField
-        Contains the frequencies at which opacities are calculated. Also holds the resulting opacity information.
+    tracing_nus : astropy.unit.quantity.Quantity
+        Numpy array of frequencies used for ray tracing with units of Hz.
     opacity_config : tardis.io.config_reader.Configuration
         Opacity section of the STARDIS configuration.
 
@@ -552,61 +548,59 @@ def calc_alphas(
     alphas : numpy.ndarray
         Array of shape (no_of_depth_points, no_of_frequencies). Total opacity at
         each depth point for each frequency in tracing_nus.
+    gammas : numpy.ndarray
+        Array of shape (no_of_lines, no_of_depth_points). Collisional broadening
+        parameter of each line at each depth point.
+    doppler_widths : numpy.ndarray
+        Array of shape (no_of_lines, no_of_depth_points). Doppler width of each
+        line at each depth point.
     """
 
     alpha_file = calc_alpha_file(
         stellar_plasma,
         stellar_model,
-        stellar_radiation_field.frequencies,
+        tracing_nus,
         opacity_config.file,
     )
-    stellar_radiation_field.opacities.opacities_dict["alpha_file"] = alpha_file
-
     alpha_bf = calc_alpha_bf(
         stellar_plasma,
         stellar_model,
-        stellar_radiation_field.frequencies,
+        tracing_nus,
         opacity_config.bf,
     )
-    stellar_radiation_field.opacities.opacities_dict["alpha_bf"] = alpha_bf
-
     alpha_ff = calc_alpha_ff(
         stellar_plasma,
         stellar_model,
-        stellar_radiation_field.frequencies,
+        tracing_nus,
         opacity_config.ff,
     )
-    stellar_radiation_field.opacities.opacities_dict["alpha_ff"] = alpha_ff
-
     alpha_rayleigh = calc_alpha_rayleigh(
         stellar_plasma,
         stellar_model,
-        stellar_radiation_field.frequencies,
+        tracing_nus,
         opacity_config.rayleigh,
     )
-    stellar_radiation_field.opacities.opacities_dict["alpha_rayleigh"] = alpha_rayleigh
-
     alpha_electron = calc_alpha_electron(
         stellar_plasma,
         stellar_model,
-        stellar_radiation_field.frequencies,
+        tracing_nus,
         opacity_config.disable_electron_scattering,
     )
-    stellar_radiation_field.opacities.opacities_dict["alpha_electron"] = alpha_electron
-
     alpha_line_at_nu, gammas, doppler_widths = calc_alpha_line_at_nu(
         stellar_plasma,
         stellar_model,
-        stellar_radiation_field.frequencies,
+        tracing_nus,
         opacity_config.line,
     )
-    stellar_radiation_field.opacities.opacities_dict[
-        "alpha_line_at_nu"
-    ] = alpha_line_at_nu
-    stellar_radiation_field.opacities.opacities_dict["alpha_line_at_nu_gammas"] = gammas
-    stellar_radiation_field.opacities.opacities_dict[
-        "alpha_line_at_nu_doppler_widths"
-    ] = doppler_widths
-    alphas = stellar_radiation_field.opacities.calc_total_alphas()
-
-    return alphas
+
+    alphas = (
+        alpha_file
+        + alpha_bf
+        + alpha_ff
+        + alpha_rayleigh
+        + alpha_electron
+        + alpha_line_at_nu
+    )
+
+    ### TODO create opacity_dict to return
+    return alphas, gammas, doppler_widths

stardis/radiation_field/opacities/opacities_solvers/broadening.py → stardis/opacities/broadening.py

@@ -30,7 +30,7 @@ def _calc_doppler_width(nu_line, temperature, atomic_mass):
     nu_line : float
         Frequency of line being considered.
     temperature : float
-        Temperature of depth points being considered.
+        Temperature of depth point being considered.
     atomic_mass : float
         Atomic mass of element being considered in grams.
 
@@ -188,7 +188,7 @@ def calc_gamma_linear_stark(n_eff_upper, n_eff_lower, electron_density):
     n_eff_lower : float
         Effective principal quantum number of lower level of transition.
     electron_density : float
-        Electron density at depth point being considered.
+        Electron density in depth point being considered.
 
     Returns
     -------
@@ -232,7 +232,7 @@ def calc_gamma_quadratic_stark(
     electron_density : float
         Electron density at depth point being considered.
     temperature : float
-        Temperature of depth points being considered.
+        Temperature of depth point being considered.
 
     Returns
     -------
@@ -280,7 +280,7 @@ def calc_gamma_van_der_waals(
     n_eff_lower : float
         Effective principal quantum number of lower level of transition.
     temperature : float
-        Temperature of depth points being considered.
+        Temperature of depth point being considered.
     h_density : float
         Number density of Hydrogen at depth point being considered.
     h_mass : float
@@ -329,7 +329,7 @@ def calc_gamma(
 ):
     """
     Calculates total collision broadening parameter for a specific line
-    and depth points.
+    and depth point.
 
     Parameters
     ----------
@@ -348,7 +348,7 @@ def calc_gamma(
     electron_density : float
         Electron density at depth point being considered.
     temperature : float
-        Temperature of depth points being considered.
+        Temperature of depth point being considered.
     h_density : float
         Number density of Hydrogen at depth point being considered.
     h_mass : float
@@ -440,7 +440,7 @@ def calculate_broadening(
     line_cols : dict
         Matches the name of a quantity to its column index in lines_array.
     no_depth_points : int
-        Number of depth pointss.
+        Number of depth points.
     atomic_masses : numpy.ndarray
         Atomic mass of all elements included in the simulation.
     electron_densities : numpy.ndarray
@@ -467,10 +467,10 @@ def calculate_broadening(
     line_nus : numpy.ndarray
         Frequency of each line.
     gammas : numpy.ndarray
-        Array of shape (no_of_lines, no_depth_points). Collisional broadening
+        Array of shape (no_of_lines, no_of_depth_points). Collisional broadening
         parameter of each line at each depth point.
     doppler_widths : numpy.ndarray
-        Array of shape (no_of_lines, no_depth_points). Doppler width of each
+        Array of shape (no_of_lines, no_of_depth_points). Doppler width of each
         line at each depth point.
     """
 

stardis/radiation_field/opacities/tests/test_broadening.py → stardis/opacities/tests/test_broadening.py

@@ -3,7 +3,7 @@
 from astropy import constants as const
 from numba import cuda
 
-from stardis.radiation_field.opacities.opacities_solvers.broadening import (
+from stardis.opacities.broadening import (
     calc_doppler_width,
     _calc_doppler_width_cuda,
     calc_doppler_width_cuda,