Merge remote-tracking branch 'upstream/main' into add_individual_inte…

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tardis-sn · Dec 18, 2024 · 8d8984c · 8d8984c
2 parents 5fbf7c3 + 1e7fbaa
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diff --git a/benchmarks/benchmark_config.yml b/benchmarks/benchmark_config.yml
@@ -15,5 +15,4 @@ opacity:
     line:
         disable: False
         broadening: [radiation, linear_stark, quadratic_stark, van_der_waals]
-        broadening_range: 3 AA
 no_of_thetas: 20
diff --git a/docs/Custom_Star_Model_with_Marcs/Custom_Star_Model_with_Marcs.ipynb b/docs/Custom_Star_Model_with_Marcs/Custom_Star_Model_with_Marcs.ipynb
@@ -1,5 +1,12 @@
 {
  "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Custom Star Model"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -12,7 +19,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Using MARCS to get .mod files\n",
+    "## Using MARCS to get .mod files\n",
     "\n",
     "STARDIS uses files from the [MARCS site](https://marcs.oreme.org/), which \"contains about 52,000 stellar atmospheric models of spectral types F, G and K\". Here we will only be discussing the aspects of MARCS needed for STARDIS. To get started, [go to the 'Search Marcs' tab of the MARCS site](https://marcs.oreme.org/data/)"
    ]
@@ -89,7 +96,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "#### One last thing: gzipped files\n",
+    "## gzipped files\n",
     "\n",
     "when you download a mod file from MARCS, it will be gzipped (shown by the file ending with '.mod.gz'). By default STARDIS will assume you have extracted the file, however you can add a line to the yaml file 'gzipped: True' as shown below and STARDIS will take care of this for you.\n",
     "\n",
@@ -104,6 +111,11 @@
     "\n",
     "```"
    ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": []
   }
  ],
  "metadata": {

diff --git a/docs/Custom_atomic_data/Custom_atomic_data.ipynb b/docs/Custom_atomic_data/Custom_atomic_data.ipynb
@@ -1,5 +1,12 @@
 {
  "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Custom Atomic Data"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -53,7 +60,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Using VALD linelists\n",
+    "## Using VALD linelists\n",
     "\n",
     "Possibly one of the most important reasons you would want to use a custom atomic data file would be to take advantage of a tailored VALD linelist. You can refer to [VALD's documentation](https://www.astro.uu.se/valdwiki) for information on these lists if you are unfamiliar. To create a detailed and accurate stellar spectrum, we highly recommend looking into using a VALD linelist bundled into your atomic data."
    ]

diff --git a/docs/index.rst b/docs/index.rst
@@ -5,19 +5,24 @@ This is the documentation for STARDIS.
 
 .. toctree::
    :maxdepth: 2
-   :caption: Contents:
 
-   Quickstart <quickstart/quickstart>
    Downloading and Installation <installation>
+   Quickstart <quickstart/quickstart>
    Physics of STARDIS <physics/physics_of_stardis>
+   Contributing <contributing>
+   Bibliography <bibliography>
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Example Notebooks
+
    Custom Atomic Data <Custom_atomic_data/Custom_atomic_data>
    Possible STARDIS Outputs <possible_stardis_outputs/possible_stardis_outputs>
    Custom Star Model <Custom_Star_Model_with_Marcs/Custom_Star_Model_with_Marcs>
    Using STARDIS in Parallel <using_stardis_in_parallel/stardis_in_parallel>
    Changing Parameters <Changing_Parameters/Changing_Parameters>
-   Example Notebooks <example_notebooks/rotation_broadening>
-   Contributing <contributing>
-   Bibliography <bibliography>
+   Rotation Broadening <rotation_broadening/rotation_broadening>
+
 
 Indices and tables
 ==================

diff --git a/docs/possible_stardis_outputs/possible_stardis_outputs.ipynb b/docs/possible_stardis_outputs/possible_stardis_outputs.ipynb
@@ -1,5 +1,12 @@
 {
  "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Possible STARDIS Outputs"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -25,13 +32,15 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "#### STARDIS simulations contain a variety of information, and depending on your needs you can have different parts of a simulation returned."
+    "## Selecting Result Options"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
+    "STARDIS simulations contain a variety of information, and depending on your needs you can have different parts of a simulation returned.\n",
+    "\n",
     "There are three parts of the simulation you can choose to return:\n",
     "- Stellar_Model\n",
     "- Stellar_Plasma\n",
@@ -40,13 +49,6 @@
     "Regardless of which are set to return, the simulation will always produce the stellar spectrum (such as the one displayed in the quickstart notebook)."
    ]
   },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "## Selecting Result Options"
-   ]
-  },
   {
    "cell_type": "markdown",
    "metadata": {},

diff --git a/docs/quickstart/quickstart.ipynb b/docs/quickstart/quickstart.ipynb
@@ -122,7 +122,6 @@
     "    line: # settings for line interaction opacity, at least one subfield is required\n",
     "        disable: <True or False>\n",
     "        broadening: <list of non-thermal broadening sources considered> # may include radiation, linear_stark, quadratic_stark, and/or van_der_waals, omit or use [] for none\n",
-    "        broadening_range: <maximum distance in frquency space to the resonant frequency for line broadening to be considered> # necessary for computational efficiency and must have units, 1e13 Hz recommended\n",
     "no_of_thetas: <number of angles to sample for raytracing>\n",
     "```\n",
     "\n",

diff --git a/...ample_notebooks/rotation_broadening.ipynb → ...tion_broadening/rotation_broadening.ipynb b/...ample_notebooks/rotation_broadening.ipynb → ...tion_broadening/rotation_broadening.ipynb
@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# STARDIS"
+    "# Rotation Broadening"
    ]
   },
   {
@@ -92,7 +92,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### STARDIS contains a post-simulation function to broaden the spectrum appropriate for a v sin(i) given by the user. However, this is only physically valid when the spectrum broadened is given over a small range of frequencies or wavelengths, or is constant in velocity resolution across the spectrum. \n",
+    "STARDIS contains a post-simulation function to broaden the spectrum appropriate for a v sin(i) given by the user. However, this is only physically valid when the spectrum broadened is given over a small range of frequencies or wavelengths, or is constant in velocity resolution across the spectrum. \n",
     "\n",
     "First, let's run a small, simple STARDIS simulation with a spectral resolution $R \\sim 100000$"
    ]

diff --git a/..._notebooks/rotation_broadening_config.yml → ...broadening/rotation_broadening_config.yml b/..._notebooks/rotation_broadening_config.yml → ...broadening/rotation_broadening_config.yml
diff --git a/docs/using_stardis_in_parallel/stardis_in_parallel.ipynb b/docs/using_stardis_in_parallel/stardis_in_parallel.ipynb
@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Setting number of threads used in running a STARDIS simulation"
+    "# Using STARDIS in Parallel"
    ]
   },
   {

diff --git a/stardis/config_schema.yml b/stardis/config_schema.yml
@@ -114,10 +114,6 @@ properties:
                         type: boolean
                         default: false
                         description: Whether to disable microturbulence.
-                    broadening_range:
-                        type: [quantity, "null"]
-                        default: null
-                        description: How far away to look for lines at any given wavelength or frequency. Must be in frequency or wavelength units. Does not apply to hydrogen. 
                     vald_linelist:
                         type: object
                         default: {}
@@ -129,6 +125,9 @@ properties:
                             shortlist:
                                 type: boolean
                                 default: false
+                            use_vald_broadening:
+                                type: boolean
+                                default: true
                         description: Options for whether to use a vald linelist. Linelist must be included the atom_data and cannot be supplied separately. 
                     include_molecules:
                         type: boolean
@@ -154,8 +153,8 @@ properties:
                 default: false
             return_radiation_field:
                 type: boolean
-                default: false
-        description: Options for what to return from the simulation. Note that return_radiation_field can be very memory intensive because it returns the intensity at every depth point, wavelength, and theta in the model.
+                default: true
+        description: Options for what to return from the simulation.
     required:
     - stardis_config_version
     - atom_data

diff --git a/stardis/conftest.py b/stardis/conftest.py
@@ -257,7 +257,6 @@ def example_stellar_radiation_field_parallel(
         stellar_model=example_stellar_model,
         stellar_radiation_field=stellar_radiation_field,
         opacity_config=example_config_parallel.opacity,
-        n_threads=example_config_parallel.n_threads,
     )
 
     raytrace(

diff --git a/stardis/plasma/base.py b/stardis/plasma/base.py
@@ -311,9 +311,9 @@ def calculate(
         linelist["level_energy_upper"] = ((linelist["e_up"].values * u.eV).cgs).value
 
         # Radiation broadening parameter is approximated as the einstein A coefficient. Vald parameters are in log scale.
-        linelist["A_ul"] = 10 ** (linelist["rad"]) / (
-            4 * np.pi
-        )  # see 1995A&AS..112..525P for appropriate units - may be off by a factor of 4pi
+        linelist["A_ul"] = 10 ** (
+            linelist["rad"]
+        )  # see 1995A&AS..112..525P for appropriate units
 
         # Need to remove autoionization lines - can't handle with current broadening treatment because can't calculate effective principal quantum number
         valid_indices = linelist.level_energy_upper < linelist.ionization_energy
@@ -449,14 +449,10 @@ def calculate(
         linelist["level_energy_upper"] = ((linelist["e_up"].values * u.eV).cgs).value
 
         # Radiation broadening parameter is approximated as the einstein A coefficient. Vald parameters are in log scale.
-        linelist["A_ul"] = 10 ** (linelist["rad"]) / (
-            4 * np.pi
-        )  # see 1995A&AS..112..525P for appropriate units - may be off by a factor of 4pi
-
-        # Need to remove autoionization lines - can't handle with current broadening treatment because can't calculate effective principal quantum number
-        valid_indices = linelist.level_energy_upper < linelist.ionization_energy
-
-        return alphas[valid_indices], linelist[valid_indices]
+        linelist["A_ul"] = 10 ** (
+            linelist["rad"]
+        )  # see 1995A&AS..112..525P for appropriate units
+        return alphas, linelist
 
 
 # Properties that haven't been used in creating stellar plasma yet,

diff --git a/stardis/plasma/molecules.py b/stardis/plasma/molecules.py
@@ -288,9 +288,9 @@ def calculate(
         linelist["level_energy_upper"] = ((linelist["e_up"].values * u.eV).cgs).value
 
         # Radiation broadening parameter is approximated as the einstein A coefficient. Vald parameters are in log scale.
-        linelist["A_ul"] = 10 ** (linelist["rad"]) / (
-            4 * np.pi
-        )  # see 1995A&AS..112..525P for appropriate units - may be off by a factor of 4pi
+        linelist["A_ul"] = 10 ** (
+            linelist["rad"]
+        )  # see 1995A&AS..112..525P for appropriate units
 
         return alphas, linelist
 
@@ -414,8 +414,8 @@ def calculate(
         linelist["level_energy_upper"] = ((linelist["e_up"].values * u.eV).cgs).value
 
         # Radiation broadening parameter is approximated as the einstein A coefficient. Vald parameters are in log scale.
-        linelist["A_ul"] = 10 ** (linelist["rad"]) / (
-            4 * np.pi
-        )  # see 1995A&AS..112..525P for appropriate units - may be off by a factor of 4pi
+        linelist["A_ul"] = 10 ** (
+            linelist["rad"]
+        )  # see 1995A&AS..112..525P for appropriate units
 
         return alphas, linelist
diff --git a/stardis/radiation_field/base.py b/stardis/radiation_field/base.py
@@ -116,7 +116,6 @@ def create_stellar_radiation_field(tracing_nus, stellar_model, stellar_plasma, c
         stellar_model=stellar_model,
         stellar_radiation_field=stellar_radiation_field,
         opacity_config=config.opacity,
-        n_threads=config.n_threads,
     )
     logger.info("Raytracing")
     raytrace(