tardis-sn · andrewfullard · Aug 18, 2023 · Feb 27, 2023 · Feb 27, 2023 · Feb 28, 2023
diff --git a/.mailmap b/.mailmap
@@ -169,6 +169,9 @@ Sampark Sharma <[email protected]>
 Shilpi Prasad <[email protected]>
 Shilpi Prasad <[email protected]> Shilpi <[email protected]>
 
+Shreyas Singh <[email protected]>
+Shreyas Singh <[email protected]> shreyas3156 <[email protected]>
+
 Satwik Kambham <[email protected]>
 Satwik Kambham <[email protected]> code-explorer <[email protected]>
 

diff --git a/docs/physics/intro/index.rst b/docs/physics/intro/index.rst
@@ -11,7 +11,7 @@ The goal of TARDIS is, given input information about a supernova, to determine (
 
 The physics of TARDIS is in four major parts, which are summarized here and in the diagram below. First, the TARDIS simulation is set up (:doc:`../setup/index`) from a TARDIS configuration (see :doc:`here <../../io/configuration/read_configuration>` for how the configuration is created). This involves the creation of the supernova model and the initial conditions of the supernova's plasma, as well as initializing the Monte Carlo runner. Next is the Monte Carlo Iteration (:doc:`../montecarlo/index`) where the heart of TARDIS takes place; packets of light are sent through the supernova and tracked as they interact with matter. Next, TARDIS uses information from the Monte Carlo iteration to update properties of the plasma to eventually find the correct plasma state (:doc:`../update_and_conv/update_and_conv`). This process of doing a Monte Carlo iteration and then updating the plasma is repeated for a specified number of times or until certain aspects of the plasma state converge (as is also discussed in :doc:`../update_and_conv/update_and_conv`). After that, data generated in the Monte Carlo simulation is used to synthesize the output spectrum of the supernova (:doc:`../spectrum/index`).
 
-In the diagram, each physics step is shown in a box with the name of the step (bolded and underlined) along with the method that triggers the step (italicized) and the major components of the step. The reading of the configuration and the overall itterative process (comprising the Monte Carlo Iteration step and Updating Plasma and Convergence step) are also shown, again with the methods triggering these processes in italics.
+In the diagram, each physics step is shown in a box with the name of the step (bolded and underlined) along with the method that triggers the step (italicized) and the major components of the step. The reading of the configuration and the overall iterative process (comprising the Monte Carlo Iteration step and Updating Plasma and Convergence step) are also shown, again with the methods triggering these processes in italics.
 
 .. graphviz:: tardis_flowchart.dot
 

diff --git a/docs/physics/intro/light_and_matter.rst b/docs/physics/intro/light_and_matter.rst
@@ -122,4 +122,4 @@ where :math:`\alpha` is called the **opacity**. Note that for our purposes, the
 
 We can interpret this in the following way: prior to traveling a distance :math:`d`, a photon will have had a :math:`e^{-\alpha d}` probability of *not* interacting with matter (and thus a :math:`1-e^{-\alpha d}` probability of having gone through an interaction). As you would expect, the larger the distance, the more likely it is that a photon interacts prior to traveling that distance, since it would have "more opportunities" to interact. Additionally, a higher :math:`\alpha` means a photon has a higher likelihood of interacting. So, more dense materials, for example, have a higher :math:`\alpha` since there is more matter for the light to interact with. Because :math:`\alpha` must take into account all three types of light-matter interactions, many of which depend on the frequency of light, it can be very difficult to calculate -- this is one of TARDIS's main tasks.
 
-Finally, the term :math:`\alpha d` has a special name: the **optical depth** :math:`\tau`. It is a dimensionless quantity that gives information about how likely it is for a photon to have gone through an interaction. Specifically, there is a :math:`1-e^{-1}\approx 63.2\%` of a photon interacting prior to traveling an optical depth of 1. The actual distance required to travel and optical depth of 1 depends on :math:`\alpha` and thus the material and the frequency of the light.
+Finally, the term :math:`\alpha d` has a special name: the **optical depth** :math:`\tau`. It is a dimensionless quantity that gives information about how likely it is for a photon to have gone through an interaction. Specifically, there is a :math:`1-e^{-1}\approx 63.2\%` of a photon interacting prior to traveling an optical depth of 1. The actual distance required to travel an optical depth of 1 depends on :math:`\alpha` and thus the material and the frequency of the light.
diff --git a/docs/physics/montecarlo/basicprinciples.rst b/docs/physics/montecarlo/basicprinciples.rst
@@ -26,7 +26,7 @@ emitted spectrum (see :ref:`spectrum`).
 Random Sampling Basics
 ======================
 
-During both the initialization of these photons and their propagation through the ejecta are modeled through
+Both the initialization of these photons and their propagation through the ejecta are modeled through
 probabilistic processes. This involves assigning probabilities to the occurrence of certain events or properties.
 For example, during isotropic scattering, finding a photon scattering into any given direction is equally likely.
 During the Monte Carlo simulation, assignments

diff --git a/docs/physics/montecarlo/lineinteraction.rst b/docs/physics/montecarlo/lineinteraction.rst
@@ -8,7 +8,7 @@ TARDIS currently offers different ways to handle line interactions, which may be
 activated via the :term:`YAML` configuration file. Independently of the chosen
 treatment, a number of steps are always carried out when a Monte Carlo packet
 performs a line interaction. Since TARDIS adopts the indivisible energy packet
-formalism (see :ref:`Energy Packets <initialization>`), the packet will have the
+formalism (see :doc:`Energy Packets <initialization>`), the packet will have the
 same energy in the co-moving frame after (f for final) the line interaction as
 before (i for initial). Thus, after accounting for the frame transformations,
 

diff --git a/docs/physics/setup/model.ipynb b/docs/physics/setup/model.ipynb
@@ -123,7 +123,7 @@
    "id": "1ee56110",
    "metadata": {},
    "source": [
-    "Notice that `radius = velocity*time_explosion`, and similarly for `r_inner`, `r_outer`, and `r_middle`. You can get the radius of the photosphere via `v_inner_boundary*time_explosion` and outer edge of the supernova via `v_outer_boundary*time_explosion`.\n",
+    "Notice that `radius = velocity*time_explosion`, and similarly for `r_inner`, `r_outer`, and `r_middle`. You can get the radius of the photosphere via `v_boundary_inner*time_explosion` and outer edge of the supernova via `v_boundary_outer*time_explosion`.\n",
     "\n",
     "<div class=\"alert alert-info\">\n",
     "    \n",
@@ -616,7 +616,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.13"
+   "version": "3.8.16"
   }
  },
  "nbformat": 4,
Original file line number	Diff line number	Diff line change
Expand Up		@@ -122,4 +122,4 @@ where :math:`\alpha` is called the opacity. Note that for our purposes, the

		We can interpret this in the following way: prior to traveling a distance :math:`d`, a photon will have had a :math:`e^{-\alpha d}` probability of not interacting with matter (and thus a :math:`1-e^{-\alpha d}` probability of having gone through an interaction). As you would expect, the larger the distance, the more likely it is that a photon interacts prior to traveling that distance, since it would have "more opportunities" to interact. Additionally, a higher :math:`\alpha` means a photon has a higher likelihood of interacting. So, more dense materials, for example, have a higher :math:`\alpha` since there is more matter for the light to interact with. Because :math:`\alpha` must take into account all three types of light-matter interactions, many of which depend on the frequency of light, it can be very difficult to calculate -- this is one of TARDIS's main tasks.

		Finally, the term :math:`\alpha d` has a special name: the optical depth :math:`\tau`. It is a dimensionless quantity that gives information about how likely it is for a photon to have gone through an interaction. Specifically, there is a :math:`1-e^{-1}\approx 63.2\%` of a photon interacting prior to traveling an optical depth of 1. The actual distance required to travel and optical depth of 1 depends on :math:`\alpha` and thus the material and the frequency of the light.
		Finally, the term :math:`\alpha d` has a special name: the optical depth :math:`\tau`. It is a dimensionless quantity that gives information about how likely it is for a photon to have gone through an interaction. Specifically, there is a :math:`1-e^{-1}\approx 63.2\%` of a photon interacting prior to traveling an optical depth of 1. The actual distance required to travel an optical depth of 1 depends on :math:`\alpha` and thus the material and the frequency of the light.