Merge branch 'main' into investigate_continuum_deficit

docs/physics/media/bound_free_absorbtion.tex

@@ -1,14 +1,14 @@
-\documentclass[convert,tikz]{standalone}
+\documentclass[convert,margin=5mm,tikz]{standalone}
 \usepackage{tikz-feynman}
 \usepackage{tikz}
 \begin{document}
 \begin{tikzpicture}
-  \filldraw[fill=blue, draw=blue, outer sep = 3px] (0,0) circle (15px) node[label=below right:Nucleus]{};%{\small Nucleus};
-  \path[densely dotted, draw=blue] (0,0) circle (105px);
+  \filldraw[fill=blue, draw=blue, outer sep = 3px] (0,0) circle (10px) node[label=below right:Nucleus]{};%{\small Nucleus};
+  \path[densely dotted, draw=blue] (0,0) circle (70px);
   % \filldraw[fill=blue, draw=blue] (-79px, 70px) circle (3px) node[anchor=north west]{\tiny \(e^-\)};
-  \node[circle,minimum size=5px, radius=5px,fill=blue, draw=blue, label=below right:\(e^-\)] (e1) at (-79px, 70px) {} ;
-  \draw[->,decorate, decoration=snake, draw=yellow] (-180px, 90px) node[anchor=south east]{\tiny Photon} -- (e1);
-  \node[circle, radius=5px,fill=blue, draw=blue, label=below:\phantom{\(e^-\)}] (e2) at (10px, 200px) {} ;
+  \node[circle,minimum size=5px, radius=5px,fill=blue, draw=blue, label=below right:\(e^-\)] (e1) at (-35px, 60px) {} ;
+  \draw[->,decorate, decoration=snake, draw=yellow] (-120px, 60px) node[anchor=south east]{\small Photon} -- (e1);
+  \node[circle, radius=5px,fill=blue, draw=blue, label=below:\phantom{\(e^-\)}] (e2) at (6px, 130px) {} ;
   \draw[->, draw=blue] (e1) -- (e2);
 \end{tikzpicture}
 \end{document}

docs/physics/media/electron_scattering.tex

@@ -7,9 +7,9 @@
   %\filldraw[fill=blue, draw=blue, outer sep = 7px] (0,0) circle (7px) node[label=right:\(e^-\)]{} ;
   % \path[densely dotted, draw=blue] (0,0) circle (105px);
   % \filldraw[fill=blue, draw=blue] (-79px, 70px) circle (3px) node[anchor=north west]{\tiny \(e^-\)};
-  \node[circle, fill=blue, draw=blue,label={right:\(e^-\)}] (e1) at (-41px, 63px) {} ;
-  \draw[->,decorate, decoration=snake, draw=yellow] (-180px, 90px) node[anchor=south east]{} -- (e1);
-  \node[] (e2) at (10px, 200px) {} ;
+  \node[circle, fill=blue, radius=5px, draw=blue,label={right:\(e^-\)}] (e1) at (-50px, 63px) {} ;
+  \draw[->,decorate, decoration=snake, draw=yellow] (-230px, 90px) node[anchor=south east]{} -- (e1);
+  \node[] (e2) at (50px, 230px) {} ;
   \draw[->,decorate, decoration=snake, draw=yellow] (e1) -- (e2);
 \end{tikzpicture}
 \end{document}

docs/physics/media/free_free_absorbtion.tex

@@ -1,10 +1,10 @@
-\documentclass[convert,tikz]{standalone}
+\documentclass[convert, margin=5mm,tikz]{standalone}
 \usepackage{tikz-feynman}
 \usepackage{tikz}
 \begin{document}
 \begin{tikzpicture}
-  \filldraw[fill=blue, draw=blue, outer sep = 25px] (0,0) circle (50px) node[label=right:Ion]{};
-  \node[circle,minimum size=5px, radius=5px,fill=blue, draw=blue, label=right:\(e^-\)] (e1) at (-79px, 70px) {} ;
-  \draw[->,decorate, decoration=snake, draw=yellow] (-180px, 70px) node[anchor=south east]{} -- (e1);
+  \filldraw[fill=blue, draw=blue, outer sep = 15px] (0,0) circle (30px) node[label=right:Ion]{};
+  \node[circle,minimum size=5px, radius=5px,fill=blue, draw=blue, label=right:\(e^-\)] (e1) at (-50px, 45px) {} ;
+  \draw[->,decorate, decoration=snake, draw=yellow] (-120px, 45px) node[anchor=south east]{} -- (e1);
 \end{tikzpicture}
 \end{document}

docs/physics/media/line_interaction.tex

@@ -1,15 +1,15 @@
-\documentclass[convert,tikz]{standalone}
+\documentclass[convert, margin=5mm, tikz]{standalone}
 \usepackage{tikz-feynman}
 \usepackage{tikz}
 \begin{document}
 \begin{tikzpicture}
-  \filldraw[fill=blue, draw=blue, outer sep = 3px] (0,0) circle (15px) node[label=below right:Nucleus]{};%{\small Nucleus};
-  \path[densely dotted, draw=blue] (0,0) circle (150px);
-    \path[densely dotted, draw=blue] (0,0) circle (200px);
+  \filldraw[fill=blue, draw=blue, outer sep = 3px] (0,0) circle (10px) node[label=below right:Nucleus]{};%{\small Nucleus};
+  \path[densely dotted, draw=blue] (0,0) circle (70px);
+    \path[densely dotted, draw=blue] (0,0) circle (90px);
   % \filldraw[fill=blue, draw=blue] (-79px, 70px) circle (3px) node[anchor=north west]{\tiny \(e^-\)};
-  \node[circle,minimum size=5px, radius=5px,fill=blue, draw=blue, label=below right:\(e^-\)] (e1) at (-80px, 125px) {} ;
-  \draw[->,decorate, decoration=snake, draw=yellow] (-400px, 90px) node[anchor=south east]{} -- (e1);
-  \node[circle, radius=5px,fill=blue, draw=blue, label=below:\phantom{\(e^-\)}] (e2) at (10px, 200px) {} ;
+  \node[circle,minimum size=5px, radius=5px,fill=blue, draw=blue, label=below right:\(e^-\)] (e1) at (-35px, 60px) {} ;
+  \draw[->,decorate, decoration=snake, draw=yellow] (-150px, 60px) node[anchor=south east]{} -- (e1);
+  \node[circle, radius=5px,fill=blue, draw=blue, label=below:\phantom{\(e^-\)}] (e2) at (10px, 90px) {} ;
   \draw[->, draw=blue] (e1) -- (e2);
 \end{tikzpicture}
 \end{document}

docs/physics/media/model_and_plasma.tex

@@ -1,14 +1,14 @@
-\documentclass[convert,tikz]{standalone}
+\documentclass[convert,margin=5mm,tikz]{standalone}
 \usepackage{tikz-feynman}
 \usepackage{tikz}
 \begin{document}
 \begin{tikzpicture}
-  \draw[ultra thick] (0,0) circle (200px);
-  \draw[ultra thick] (0,0) circle (175px);
-  \draw[ultra thick] (0,0) circle (150px);
-  \draw[ultra thick] (0,0) circle (125px);
-  \filldraw[fill=orange!50!white, draw=orange, ultra thick] (0,0) circle (100px);
+  \draw[] (0,0) circle (115px);
+  \draw[] (0,0) circle (105px);
+  \draw[] (0,0) circle (95px);
+  \draw[] (0,0) circle (85px);
+  \filldraw[fill=orange!50!white, draw=orange, ultra thick] (0,0) circle (75px);
   \node[] (inner) {Inner boundary of atmosphere} (0, 0);
-  \node[] at (8, -5) (outer) {Outer boundary of atmosphere};
+  \node[] at (5.5, -3) (outer) {Outer boundary of atmosphere};
 \end{tikzpicture}
 \end{document}

docs/physics/media/rayleigh_scattering.tex

@@ -1,15 +1,15 @@
-\documentclass[convert,tikz]{standalone}
+\documentclass[convert, margin=5mm, tikz]{standalone}
 \usepackage{tikz-feynman}
 \usepackage{tikz}
 %\usetikzlibrary{animations}
 \begin{document}
 \begin{tikzpicture}
-  \filldraw[fill=blue, draw=blue, outer sep = 35px] (0,0) circle (75px) node[label=right:Atom/Molecule]{};%{\small Nucleus};
+  \filldraw[fill=blue, draw=blue, outer sep = 12px] (0,0) circle (30px) node[label=right:Atom/Molecule]{};%{\small Nucleus};
   % \path[densely dotted, draw=blue] (0,0) circle (105px);
   % \filldraw[fill=blue, draw=blue] (-79px, 70px) circle (3px) node[anchor=north west]{\tiny \(e^-\)};
-  \node[] (e1) at (-41px, 63px) {} ;
-  \draw[->,decorate, decoration=snake, draw=yellow] (-180px, 90px) node[anchor=south east]{} -- (e1);
-  \node[] (e2) at (10px, 200px) {} ;
+  \node[] (e1) at (-15px, 25px) {} ;
+  \draw[->,decorate, decoration=snake, draw=yellow] (-80px, 50px) node[anchor=south east]{} -- (e1);
+  \node[] (e2) at (10px, 80px) {} ;
   \draw[->,decorate, decoration=snake, draw=yellow] (e1) -- (e2);
 \end{tikzpicture}
 \end{document}

stardis/base.py

@@ -87,7 +87,10 @@ def run_stardis(config_fname, tracing_lambdas_or_nus):
                 ]
             )
             + 1,
-        )
+        ),
+        line_interaction_type="macroatom",
+        nlte_species=[],
+        continuum_interaction_species=[],
     )
     # plasma
     stellar_plasma = create_stellar_plasma(stellar_model, adata, config)

stardis/conftest.py

@@ -73,7 +73,10 @@ def example_stellar_plasma(
                 ]
             )
             + 1,
-        )
+        ),
+        line_interaction_type="macroatom",
+        nlte_species=[],
+        continuum_interaction_species=[],
     )
     return create_stellar_plasma(
         example_stellar_model, example_kurucz_atomic_data, example_config

stardis/radiation_field/base.py

@@ -6,7 +6,6 @@ class RadiationField:
     """
     Class containing information about the radiation field.
     ###TODO Radiation field temperature should be a separate attribute, for the case of differing gas and radiation.
-    ###TODO Implement a source function class. Doesn't need to be done until we have another source function than just blackbody.
 
     Parameters
     ----------
@@ -30,5 +29,5 @@ class RadiationField:
     def __init__(self, frequencies, source_function, stellar_model):
         self.frequencies = frequencies
         self.source_function = source_function
-        self.opacities = Opacities()
-        self.F_nu = np.zeros((len(stellar_model.geometry.r), len(frequencies)))
+        self.opacities = Opacities(frequencies, stellar_model)
+        self.F_nu = np.zeros((stellar_model.no_of_depth_points, len(frequencies)))

stardis/radiation_field/opacities/base.py

@@ -1,3 +1,6 @@
+import numpy as np
+
+
 class Opacities:
     """
     Holds opacity information.
@@ -11,15 +14,15 @@ class Opacities:
         Added as an attribute when calc_total_alphas() is called.
     """
 
-    def __init__(self):
+    def __init__(self, frequencies, stellar_model):
         self.opacities_dict = {}
+        self.total_alphas = np.zeros(
+            (stellar_model.no_of_depth_points, len(frequencies))
+        )
 
     ###TODO: Better implementation for this
     def calc_total_alphas(self):
-        for i, item in enumerate(self.opacities_dict.items()):
+        for item in self.opacities_dict.items():
             if "gammas" not in item[0] and "doppler" not in item[0]:
-                if i == 0:
-                    self.total_alphas = item[1]
-                else:
-                    self.total_alphas += item[1]
+                self.total_alphas += item[1]
         return self.total_alphas