Rework Estimators and Convergence Docs (#2108)

* major changes

* fixing links

* fix link

* typo fixes

* first draft of code section

* rough draft

* fixing capitalization conventions

* many of Andrew's changes

* grammar and other small changes

* andrew's and other small changes

docs/index.rst

@@ -77,7 +77,7 @@ Mission Statement
     physics/intro/index
     physics/setup/index
     physics/montecarlo/index
-    physics/est_and_conv/index
+    physics/update_and_conv/update_and_conv
     physics/spectrum/index
     physics/energy_input/index
 

docs/io/configuration/components/models/index.rst

@@ -279,8 +279,8 @@ factor of .8, etc.
 .. note::
 
     ``t_rad`` and ``dilution_factor`` are the values of the temperature and dilution factor for the first
-    iteration, and will be updated in subsequent iterations (see :ref:`est_and_conv`). To prevent these
-    quantities from being changed, you must set the damping constant to zero in the :ref:`Damped Convergence
+    iteration, and will be updated in subsequent iterations (see :doc:`../../../../physics/update_and_conv/update_and_conv`).
+    To prevent these quantities from being changed, you must set the damping constant to zero in the :ref:`Damped Convergence
     Configuration <damped-config>` in the Monte Carlo section of the configuration file.
 
 CSVY Model Tutorial

docs/io/configuration/components/montecarlo.rst

@@ -16,7 +16,7 @@ of the Monte Carlo loop (which calculates the final spectrum!) when the radiatio
 ``no_of_packets`` to create a less noisy output spectrum. ``no_of_virtual_packets`` can also be set to greater than 0 (a useful number is 3) to
 use the Virtual Packet formalism. Increasing this number drastically increases computational costs (and memory requirements if they are logged).
 The ``iterations`` parameter describes the maximum number of Monte Carlo loops executed in a simulation before it ends. Convergence criteria can be used to make the simulation stop
-sooner when the convergence threshold has been reached (see :ref:`convergence`).
+sooner when the convergence threshold has been reached (see :doc:`../../../physics/update_and_conv/update_and_conv`).
 
 .. _conv-config:
 

docs/io/configuration/components/plasma.rst

@@ -23,7 +23,7 @@ The radiative rates describe how to calculate the :math:`J_\textrm{blue}` needed
 :math:`J_\textrm{blue} = W \times \textrm{Blackbody}(T_\textrm{rad})`
 
 3) ``detailed`` in which the :math:`J_\textrm{blue}`
-are calculated using an estimator (this is described in :doc:`../../../physics/est_and_conv/estimators`).
+are calculated using an estimator (this is described in :doc:`../../../physics/montecarlo/estimators`).
 
 TARDIS currently supports three different kinds of line interaction: ``scatter`` --- a resonance scattering implementation,
 ``macroatom`` --- the most complex form of line interaction described in :ref:`macroatom` and ``downbranch`` a simplified

docs/io/configuration/components/supernova.rst

@@ -8,7 +8,7 @@ The supernova component of the configuration file contains some key information
 
 .. jsonschema:: schemas/supernova.yml
 
-As luminosity (in units of energy/s) is computed by integrating over the spectral luminosity (in units of energy/s/wavelength), TARDIS sums over all discrete energy packets to compute luminosity when ran, attempting to converge the output spectrum to match `luminosity_requested` (see :ref:`est_and_conv`). `luminosity_requested` can be given in standard units, such as erg/s or J/s, or in logarithmic units such as log_lsun. The range over which TARDIS sums these energy packets is set by default from 0 to infinity via `luminosity_wavelength_start` and `luminosity_wavelength_end`, respectively, so as to generate a spectrum whose total luminosity across the entire spectrum is `luminosity_requested`. However, if in the event only the luminosity within a certain range of wavelengths is known, then `luminosity_wavelength_start` and `luminosity_wavelength_end` can be changed as necessary to reflect this, allowing TARDIS to attempt to create a spectrum whose luminosity within the set range will converge to the value defined in `luminosity_requested`.
+As luminosity (in units of energy/s) is computed by integrating over the spectral luminosity (in units of energy/s/wavelength), TARDIS sums over all discrete energy packets to compute luminosity when ran, attempting to converge the output spectrum to match `luminosity_requested` (see :doc:`../../../physics/update_and_conv/update_and_conv`). `luminosity_requested` can be given in standard units, such as erg/s or J/s, or in logarithmic units such as log_lsun. The range over which TARDIS sums these energy packets is set by default from 0 to infinity via `luminosity_wavelength_start` and `luminosity_wavelength_end`, respectively, so as to generate a spectrum whose total luminosity across the entire spectrum is `luminosity_requested`. However, if in the event only the luminosity within a certain range of wavelengths is known, then `luminosity_wavelength_start` and `luminosity_wavelength_end` can be changed as necessary to reflect this, allowing TARDIS to attempt to create a spectrum whose luminosity within the set range will converge to the value defined in `luminosity_requested`.
 
 As an example, here is a sample code which will generate a specturm where only the luminosity of the visible light portion of the spectrum is given. Here, the output spectrum will have a luminosity of approximately :math:`10^{9.44}L_{sun}` within the visible range.