diff --git a/Docs/source/networks.rst b/Docs/source/networks.rst
index 908a6ee20..65505aa18 100644
--- a/Docs/source/networks.rst
+++ b/Docs/source/networks.rst
@@ -2,40 +2,26 @@
Available Reaction Networks
***************************
+A network defines the composition, which is needed by the equation
+of state and transport coefficient routines. Even if there are no
+reactions taking place, a network still needs to be defined, so
+Microphysics knows the properties of the fluid.
-``iso7``, ``aprox13``, ``aprox19``, and ``aprox21``
-===================================================
-
-These are alpha-chains (with some other nuclei) from Frank Timmes.
-These networks share common rates (from ``Microphysics/rates``),
-plasma neutrino loses (from ``Microphysics/neutrinos``), and
-electron screening (from ``Microphysics/screening``).
-
-Energy generation.
-------------------
-
-These networks store the total binding energy of the nucleus in MeV as
-``bion(:)``. They then compute the mass of each nucleus in grams as:
-
-.. math:: M_k = (A_k - Z_k) m_n + Z_k (m_p + m_e) - B_k
-
-where :math:`m_n`, :math:`m_p`, and :math:`m_e` are the neutron, proton, and electron
-masses, :math:`A_k` and :math:`Z_k` are the atomic weight and number, and :math:`B_k`
-is the binding energy of the nucleus (converted to grams). :math:`M_k`
-is stored as ``mion(:)`` in the network.
-
-The energy release per gram is converted from the rates as:
+.. tip::
-.. math:: \epsilon = -N_A c^2 \sum_k \frac{dY_k}{dt} M_k - \epsilon_\nu
+ If reactions can be ignored, then the ``general_null`` network can
+ be used --- this simply defines a composition with no reactions.
-where :math:`N_A` is Avogadro’s number (to convert this to “per gram”)
-and :math:`\edotnu` is the neutrino loss term (see :ref:`neutrino_loss`).
+.. note::
+ Many of the networks here are generated using `pynucastro
+ `_ using the ``AmrexAstroCxxNetwork``
+ class.
``general_null``
================
-``general_null`` is a bare interface for a nuclear reaction network --
+``general_null`` is a bare interface for a nuclear reaction network ---
no reactions are enabled. The
data in the network is defined at compile type by specifying an
inputs file. For example,
@@ -75,29 +61,214 @@ The name of the inputs file by one of two make variables:
GENERAL_NET_INPUTS := /path/to/file/triple_alpha_plus_o.net
+.. index:: network_properties.H
+
At compile time, the "`.net`" file is parsed and a network header
``network_properties.H`` is written using the python script
``write_network.py``. The make rule for this is contained in
-``Make.package``.
+``Microphysics/networks/Make.package``.
+
+
+``iso7``, ``aprox13``, ``aprox19``, and ``aprox21``
+===================================================
+
+These are alpha-chains (with some other nuclei) based on the `original
+Fortran networks from Frank Timmes
+`_. These
+networks share common rates from ``Microphysics/rates`` and are
+implemented using the templated C++ network infrastructure.
+
+These networks approximate a lot of the links, in particular,
+combining $(\alpha, p)(p, \gamma)$ and $(\alpha, \gamma)$ into a
+single effective rate.
+
+Nuclei
+------
+
+* ``iso7`` : contains $\isotm{He}{4}$, $\isotm{C}{12}$,
+ $\isotm{O}{16}$, $\isotm{Ne}{20}$, $\isotm{Mg}{24}$, $\isotm{Si}{28}$,
+ $\isotm{Ni}{56}$ and is based on :cite:`iso7`.
+
+* ``aprox13`` : adds $\isotm{S}{32}$, $\isotm{Ar}{36}$, $\isotm{Ca}{40}$, $\isotm{Ti}{44}$, $\isotm{Cr}{48}$, $\isotm{Fe}{52}$
+
+* ``aprox19`` : adds $\isotm{H}{1}$, $\isotm{He}{3}$, $\isotm{N}{14}$, $\isotm{Fe}{54}$,
+ $\mathrm{p}$, $\mathrm{n}$. Here, $\mathrm{p}$ participates only in the photodisintegration rates at high mass number, and is distinct from $\isotm{H}{1}$.
+
+* ``aprox21`` : adds $\isotm{Cr}{56}$, $\isotm{Fe}{56}$. This is designed to reach
+ a lower $Y_e$ than the other networks, for use in massive star simulations. Note
+ that the link to $\isotm{Cr}{56}$ is greatly approximated.
+
+
+These networks store the total binding energy of the nucleus in MeV as
+``bion(:)``. They then compute the mass of each nucleus in grams as:
+
+.. math:: M_k = (A_k - Z_k) m_n + Z_k (m_p + m_e) - B_k
+
+where :math:`m_n`, :math:`m_p`, and :math:`m_e` are the neutron, proton, and electron
+masses, :math:`A_k` and :math:`Z_k` are the atomic weight and number, and :math:`B_k`
+is the binding energy of the nucleus (converted to grams). :math:`M_k`
+is stored as ``mion(:)`` in the network.
+
+The energy release per gram is converted from the rates as:
+
+.. math:: \epsilon = -N_A c^2 \sum_k \frac{dY_k}{dt} M_k - \epsilon_\nu
+
+where :math:`N_A` is Avogadro’s number (to convert this to “per gram”)
+and :math:`\edotnu` is the neutrino loss term (see :ref:`neutrino_loss`).
+
+
``CNO_extras``
==============
-This network replicates the popular [MESA "cno_extras"
-network](https://docs.mesastar.org/en/latest/net/nets.html) which is
+This network replicates the popular `MESA "cno_extras"
+network `_ which is
meant to study hot-CNO burning and the start of the breakout from CNO
-burning.
-
-We add ${}^{56}\mathrm{Fe}$ as an inert nucleus to allow this to be
-used for X-ray burst simulations.
+burning. This network is managed by pynucastro.
.. figure:: cno_extras_hide_alpha.png
:align: center
+.. note::
+
+ We add ${}^{56}\mathrm{Fe}$ as an inert nucleus to allow this to be
+ used for X-ray burst simulations (not shown in the network diagram
+ above).
+
+
+nova networks
+=============
+
+The ``nova`` and ``nova2`` networks both are intended for modeling classical novae.
+
+
+* ``nova`` focuses just on CNO/hot-CNO:
+
+ .. figure:: nova.png
+ :align: center
+
+* ``nova2`` expands ``nova`` by adding the pp-chain nuclei:
+
+ .. figure:: nova2.png
+ :align: center
+
+
+He-burning networks
+===================
+
+This is a collection of networks meant to model He burning. The are inspired by the
+"aprox"-family of networks, but contain more nuclei/rates, and are managed by
+pynucastro.
+
+One feature of these networks is that they include a bypass rate for
+:math:`\isotm{C}{12}(\alpha, \gamma)\isotm{O}{16}` discussed in
+:cite:`ShenBildsten`. This is appropriate for explosive He burning.
+
+:cite:`ShenBildsten` discuss the sequences:
+
+* :math:`\isotm{C}{14}(\alpha, \gamma)\isotm{O}{18}(\alpha,
+ \gamma)\isotm{Ne}{22}` at high temperatures (T > 1 GK). We don't
+ consider this.
+
+* :math:`\isotm{N}{14}(\alpha, \gamma)\isotm{F}{18}(\alpha,
+ p)\isotm{Ne}{21}` is the one they consider important, since it produces
+ protons that are then available for :math:`\isotm{C}{12}(p,
+ \gamma)\isotm{N}{13}(\alpha, p)\isotm{O}{16}`.
+
+This leaves :math:`\isotm{Ne}{21}` as an endpoint, which we connect to
+the other nuclei by including :math:`\isotm{Na}{22}`.
+
+For the :math:`\isotm{C}{12} + \isotm{C}{12}`, :math:`\isotm{C}{12} +
+\isotm{O}{16}`, and :math:`\isotm{O}{16} + \isotm{O}{16}` rates, we
+also need to include:
+
+* :math:`\isotm{C}{12}(\isotm{C}{12},n)\isotm{Mg}{23}(n,\gamma)\isotm{Mg}{24}`
+
+* :math:`\isotm{O}{16}(\isotm{O}{16}, n)\isotm{S}{31}(n, \gamma)\isotm{S}{32}`
+
+* :math:`\isotm{O}{16}(\isotm{C}{12}, n)\isotm{Si}{27}(n, \gamma)\isotm{Si}{28}`
+
+Since the neutron captures on those
+intermediate nuclei are so fast, we leave those out and take the
+forward rate to just be the first rate. We do not include reverse
+rates for these processes.
+
+
+``subch_simple``
+----------------
+
+``subch_simple`` uses the ideas above but approximates some
+of the rates by
+combining some of the :math:`A(\alpha,p)X(p,\gamma)B` links with
+:math:`A(\alpha,\gamma)B`, allowing us to drop the intermediate
+nucleus :math:`X`. We do this for :math:`\isotm{Cl}{35}`,
+:math:`\isotm{K}{39}`, :math:`\isotm{Sc}{43}`, :math:`\isotm{V}{47}`,
+:math:`\isotm{Mn}{51}`, and :math:`\isotm{Co}{55}`.
+
+Further simplifications include:
+
+* The reverse rates of :math:`\isotm{C}{12}+\isotm{C}{12}`,
+ :math:`\isotm{C}{12}+\isotm{O}{16}`, :math:`\isotm{O}{16}+\isotm{O}{16}` are
+ neglected since they're not present in the original aprox13 network
+
+* The :math:`\isotm{C}{12}+\isotm{Ne}{20}` rate is removed
+
+* The :math:`(\alpha, \gamma)` links between :math:`\isotm{Na}{23}`,
+ :math:`\isotm{Al}{27}` and between :math:`\isotm{Al}{27}` and
+ :math:`\isotm{P}{31}` are removed, since they're not in the
+ original aprox13 network.
+
+The network appears as:
+
+.. figure:: subch_simple.png
+ :align: center
+
+The nuclei in gray are those that have been approximated about, but the links
+are effectively accounted for in the approximate rates.
+
+.. warning:: Due to inclusion of the rate sequence,
+ ${}^{14}\mathrm{N}(\alpha, \gamma){}^{18}\mathrm{F}(\alpha,
+ \mathrm{p}){}^{21}\mathrm{Ne}$, there is an artificial end-point at
+ ${}^{22}\mathrm{Na}$.
+
+``subch_base``
+--------------
+
+``subch_base`` is the simplest subch network. It is created to reconcile the
+artificial end-point at :math:`\isotm{Na}{22}`. This is done by excluding
+:math:`\isotm{N}{14}`, :math:`\isotm{F}{18}`, :math:`\isotm{Ne}{21}`,
+and :math:`\isotm{Na}{22}`. These nuclei were added to include
+:math:`\isotm{N}{14}(\alpha, \gamma)\isotm{F}{18}(\alpha, p)\isotm{Ne}{21}`
+rate sequence, which allows an enhancement to the
+:math:`\isotm{C}{12}(p, \gamma)\isotm{N}{13}(\alpha, p)\isotm{O}{16}`
+rate due to the additional proton release. However, we find the effect is not
+extremely significant.
+
+.. figure:: subch_base.png
+ :align: center
+
+disabling rates
+---------------
+
+For all subch networks, there are 2 runtime parameters that can be used
+to disable rates:
+
+* ``network.disable_p_c12__n13`` : if set to ``1``, then the rate
+ :math:`\isotm{C}{12}(p,\gamma)\isotm{N}{13}` and its inverse are
+ disabled.
+
+* ``network.disable_he4_n13__p_o16`` : if set to ``1``, then the rate
+ :math:`\isotm{N}{13}(\alpha,p)\isotm{O}{16}` and its inverse are
+ disabled.
+
+Together, these parameters allow us to turn off the sequence
+:math:`\isotm{C}{12}(p,\gamma)\isotm{N}{13}(\alpha, p)\isotm{O}{16}` that
+acts as a bypass for :math:`\isotm{C}{12}(\alpha, \gamma)\isotm{O}{16}`.
+
``CNO_He_burn``
-===============
+---------------
This network is meant to study explosive H and He burning. It combines
the ``CNO_extras`` network (with the exception of the inert ${}^{56}\mathrm{Fe}$
@@ -116,9 +287,15 @@ It includes various weak rates that are important to this process.
.. figure:: ECSN.png
:align: center
+C-ignition networks
+===================
+
+There are a number of networks that have been developed for exploring
+carbon burning in near-Chandrasekhar mass which dwarfs.
+
``ignition_chamulak``
-=====================
+---------------------
This network was introduced in our paper on convection in white dwarfs
as a model of Type Ia supernovae :cite:`wdconvect`. It models
@@ -127,11 +304,6 @@ and captures the effects of a much larger network by setting the ash
state and energetics to the values suggested in :cite:`chamulak:2008`.
-.. _energy-generation.-1:
-
-Energy generation.
-------------------
-
The binding energy, :math:`q`, in this
network is interpolated based on the density. It is stored as the
binding energy (ergs/g) *per nucleon*, with a sign convention that
@@ -142,7 +314,7 @@ binding energies are negative. The energy generation rate is then:
(this is positive since both :math:`q` and :math:`dY/dt` are negative)
``ignition_reaclib``
-====================
+--------------------
This contains several networks designed to model C burning in WDs. They include:
@@ -158,7 +330,7 @@ This contains several networks designed to model C burning in WDs. They include
``ignition_simple``
-===================
+-------------------
This is the original network used in our white dwarf convection
studies :cite:`lowMach4`. It includes a single-step
@@ -178,22 +350,6 @@ of (Graboske 1973) for weak screening and the work of (Alastuey 1978
and Itoh 1979) for strong screening.
-nova networks
-=============
-
-The ``nova`` and ``nova2`` networks both are intended for modeling classical novae.
-
-
-* ``nova`` focuses just on CNO/hot-CNO:
-
- .. figure:: nova.png
- :align: center
-
-* ``nova2`` expands ``nova`` by adding the pp-chain nuclei:
-
- .. figure:: nova2.png
- :align: center
-
``powerlaw``
============
@@ -266,113 +422,3 @@ This network was used for the X-ray burst studies in
This is a 2 reaction network for helium burning, capturing the :math:`3`-:math:`\alpha`
reaction and :math:`\isotm{C}{12}(\alpha,\gamma)\isotm{O}{16}`. Additionally,
:math:`^{56}\mathrm{Fe}` is included as an inert species.
-
-
-subch networks
-==============
-
-The subch networks recreate an ``aprox13``
-alpha-chain + including a bypass rate for :math:`\isotm{C}{12}(\alpha,
-\gamma)\isotm{O}{16}` discussed in :cite:`ShenBildsten`. This is appropriate
-for explosive He burning.
-
-:cite:`ShenBildsten` discuss the sequences:
-
-* :math:`\isotm{C}{14}(\alpha, \gamma)\isotm{O}{18}(\alpha,
- \gamma)\isotm{Ne}{22}` at high temperatures (T > 1 GK). We don't
- consider this.
-
-* :math:`\isotm{N}{14}(\alpha, \gamma)\isotm{F}{18}(\alpha,
- p)\isotm{Ne}{21}` is the one they consider important, since it produces
- protons that are then available for :math:`\isotm{C}{12}(p,
- \gamma)\isotm{N}{13}(\alpha, p)\isotm{O}{16}`.
-
-This leaves :math:`\isotm{Ne}{21}` as an endpoint, which we connect to
-the other nuclei by including :math:`\isotm{Na}{22}`.
-
-For the :math:`\isotm{C}{12} + \isotm{C}{12}`, :math:`\isotm{C}{12} +
-\isotm{O}{16}`, and :math:`\isotm{O}{16} + \isotm{O}{16}` rates, we
-also need to include:
-
-* :math:`\isotm{C}{12}(\isotm{C}{12},n)\isotm{Mg}{23}(n,\gamma)\isotm{Mg}{24}`
-
-* :math:`\isotm{O}{16}(\isotm{O}{16}, n)\isotm{S}{31}(n, \gamma)\isotm{S}{32}`
-
-* :math:`\isotm{O}{16}(\isotm{C}{12}, n)\isotm{Si}{27}(n, \gamma)\isotm{Si}{28}`
-
-Since the neutron captures on those
-intermediate nuclei are so fast, we leave those out and take the
-forward rate to just be the first rate. We do not include reverse
-rates for these processes.
-
-
-``subch_simple``
-----------------
-
-``subch_simple`` uses the ideas above but approximates some
-of the rates by
-combining some of the :math:`A(\alpha,p)X(p,\gamma)B` links with
-:math:`A(\alpha,\gamma)B`, allowing us to drop the intermediate
-nucleus :math:`X`. We do this for :math:`\isotm{Cl}{35}`,
-:math:`\isotm{K}{39}`, :math:`\isotm{Sc}{43}`, :math:`\isotm{V}{47}`,
-:math:`\isotm{Mn}{51}`, and :math:`\isotm{Co}{55}`.
-
-Further simplifications include:
-
-* The reverse rates of :math:`\isotm{C}{12}+\isotm{C}{12}`,
- :math:`\isotm{C}{12}+\isotm{O}{16}`, :math:`\isotm{O}{16}+\isotm{O}{16}` are
- neglected since they're not present in the original aprox13 network
-
-* The :math:`\isotm{C}{12}+\isotm{Ne}{20}` rate is removed
-
-* The :math:`(\alpha, \gamma)` links between :math:`\isotm{Na}{23}`,
- :math:`\isotm{Al}{27}` and between :math:`\isotm{Al}{27}` and
- :math:`\isotm{P}{31}` are removed, since they're not in the
- original aprox13 network.
-
-The network appears as:
-
-.. figure:: subch_simple.png
- :align: center
-
-The nuclei in gray are those that have been approximated about, but the links
-are effectively accounted for in the approximate rates.
-
-.. warning:: Due to inclusion of the rate sequence,
- ${}^{14}\mathrm{N}(\alpha, \gamma){}^{18}\mathrm{F}(\alpha,
- \mathrm{p}){}^{21}\mathrm{Ne}$, there is an artificial end-point at
- ${}^{22}\mathrm{Na}$.
-
-``subch_base``
---------------
-
-``subch_base`` is the simplest subch network. It is created to reconcile the
-artificial end-point at :math:`\isotm{Na}{22}`. This is done by excluding
-:math:`\isotm{N}{14}`, :math:`\isotm{F}{18}`, :math:`\isotm{Ne}{21}`,
-and :math:`\isotm{Na}{22}`. These nuclei were added to include
-:math:`\isotm{N}{14}(\alpha, \gamma)\isotm{F}{18}(\alpha, p)\isotm{Ne}{21}`
-rate sequence, which allows an enhancement to the
-:math:`\isotm{C}{12}(p, \gamma)\isotm{N}{13}(\alpha, p)\isotm{O}{16}`
-rate due to the additional proton release. However, we find the effect is not
-extremely significant.
-
-.. figure:: subch_base.png
- :align: center
-
-disabling rates
----------------
-
-For all subch networks, there are 2 runtime parameters that can be used
-to disable rates:
-
-* ``network.disable_p_c12__n13`` : if set to ``1``, then the rate
- :math:`\isotm{C}{12}(p,\gamma)\isotm{N}{13}` and its inverse are
- disabled.
-
-* ``network.disable_he4_n13__p_o16`` : if set to ``1``, then the rate
- :math:`\isotm{N}{13}(\alpha,p)\isotm{O}{16}` and its inverse are
- disabled.
-
-Together, these parameters allow us to turn off the sequence
-:math:`\isotm{C}{12}(p,\gamma)\isotm{N}{13}(\alpha, p)\isotm{O}{16}` that
-acts as a bypass for :math:`\isotm{C}{12}(\alpha, \gamma)\isotm{O}{16}`.
diff --git a/Docs/source/refs.bib b/Docs/source/refs.bib
index 67eb16774..7975609ae 100644
--- a/Docs/source/refs.bib
+++ b/Docs/source/refs.bib
@@ -701,3 +701,18 @@ @ARTICLE{itoh:1996
adsurl = {https://ui.adsabs.harvard.edu/abs/1996ApJS..102..411I},
adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}
+
+@ARTICLE{iso7,
+ author = {{Timmes}, F.~X. and {Hoffman}, R.~D. and {Woosley}, S.~E.},
+ title = "{An Inexpensive Nuclear Energy Generation Network for Stellar Hydrodynamics}",
+ journal = {\apjs},
+ keywords = {Hydrodynamics, Methods: Numerical, Nuclear Reactions, Nucleosynthesis, Abundances, Stars: General},
+ year = 2000,
+ month = jul,
+ volume = {129},
+ number = {1},
+ pages = {377-398},
+ doi = {10.1086/313407},
+ adsurl = {https://ui.adsabs.harvard.edu/abs/2000ApJS..129..377T},
+ adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
diff --git a/Docs/source/runtime_parameters.rst b/Docs/source/runtime_parameters.rst
index e35240cd4..844ed2f81 100644
--- a/Docs/source/runtime_parameters.rst
+++ b/Docs/source/runtime_parameters.rst
@@ -1,7 +1,7 @@
Parameters by Namespace
=======================
-namespace: none
----------------
+namespace: ``cj``
+-----------------
**util/cj_detonation:**
@@ -25,7 +25,7 @@ namespace: ``conductivity``
+---------------------------------------+---------------------------------------------------------+------------------------------+
| parameter | description | default value |
+=======================================+=========================================================+==============================+
-| ``const_conductivity`` | | 1.0e0 |
+| ``const_conductivity`` | constant value of the conductivity, in erg/s/cm/K | 1.0e0 |
+---------------------------------------+---------------------------------------------------------+------------------------------+
@@ -35,7 +35,7 @@ namespace: ``conductivity``
+---------------------------------------+---------------------------------------------------------+------------------------------+
| parameter | description | default value |
+=======================================+=========================================================+==============================+
-| ``const_opacity`` | | 7.0e-2 |
+| ``const_opacity`` | opacity value, in units of cm**2/g | 7.0e-2 |
+---------------------------------------+---------------------------------------------------------+------------------------------+
@@ -45,9 +45,9 @@ namespace: ``conductivity``
+---------------------------------------+---------------------------------------------------------+------------------------------+
| parameter | description | default value |
+=======================================+=========================================================+==============================+
-| ``cond_coeff`` | | 1.0 |
+| ``cond_coeff`` | proportionality constant, C, in k = C T**m | 1.0 |
+---------------------------------------+---------------------------------------------------------+------------------------------+
-| ``cond_exponent`` | | 1.0 |
+| ``cond_exponent`` | temperature exponent, m, in k = C T**m | 1.0 |
+---------------------------------------+---------------------------------------------------------+------------------------------+
@@ -70,9 +70,11 @@ namespace: ``eos``
+---------------------------------------+---------------------------------------------------------+------------------------------+
| parameter | description | default value |
+=======================================+=========================================================+==============================+
-| ``eos_gamma`` | | 5.e0/3.e0 |
+| ``eos_gamma`` | ratio of specific heats | 5.e0/3.e0 |
+---------------------------------------+---------------------------------------------------------+------------------------------+
-| ``eos_assume_neutral`` | | 1 |
+| ``eos_assume_neutral`` | when computing mu / Abar, do we assume that the | 1 |
+| | composition is atoms or ionized, and therefore include | |
+| | the electron contributions separately? | |
+---------------------------------------+---------------------------------------------------------+------------------------------+
@@ -319,19 +321,20 @@ namespace: ``eos``
+---------------------------------------+---------------------------------------------------------+------------------------------+
| parameter | description | default value |
+=======================================+=========================================================+==============================+
-| ``eos_gamma_default`` | | 1.4 |
+| ``eos_gamma_default`` | default ratio of specific heats used for all components | 1.4 |
+| | unless specified explicitly as species a, b, or c | |
+---------------------------------------+---------------------------------------------------------+------------------------------+
-| ``species_a_name`` | | "" |
+| ``species_a_name`` | name of species "a" | "" |
+---------------------------------------+---------------------------------------------------------+------------------------------+
-| ``species_a_gamma`` | | 1.4 |
+| ``species_a_gamma`` | ratio of specific heats for species "a" | 1.4 |
+---------------------------------------+---------------------------------------------------------+------------------------------+
-| ``species_b_name`` | | "" |
+| ``species_b_name`` | name of species "b" | "" |
+---------------------------------------+---------------------------------------------------------+------------------------------+
-| ``species_b_gamma`` | | 1.4 |
+| ``species_b_gamma`` | ratio of specific heats for species "b" | 1.4 |
+---------------------------------------+---------------------------------------------------------+------------------------------+
-| ``species_c_name`` | | "" |
+| ``species_c_name`` | name of species "c" | "" |
+---------------------------------------+---------------------------------------------------------+------------------------------+
-| ``species_c_gamma`` | | 1.4 |
+| ``species_c_gamma`` | ratio of specific heats for species "c" | 1.4 |
+---------------------------------------+---------------------------------------------------------+------------------------------+
@@ -341,13 +344,18 @@ namespace: ``eos``
+---------------------------------------+---------------------------------------------------------+------------------------------+
| parameter | description | default value |
+=======================================+=========================================================+==============================+
-| ``polytrope_type`` | | 0 |
+| ``polytrope_type`` | polytrope type: 1 is non-relativistic, fully degenerate | 0 |
+| | electron gas; 2 is fully-relativistic, fully degenerate | |
+| | gas. If these are set, then only pulytrope_mu_e needs | |
+| | to be set. | |
+---------------------------------------+---------------------------------------------------------+------------------------------+
-| ``polytrope_gamma`` | | 0.0e0 |
+| ``polytrope_gamma`` | density exponent for pressure, P = K rho**gamma | 0.0e0 |
+---------------------------------------+---------------------------------------------------------+------------------------------+
-| ``polytrope_K`` | | 0.0e0 |
+| ``polytrope_K`` | proportionality constant in EOS, P = K rho**gamma | 0.0e0 |
+---------------------------------------+---------------------------------------------------------+------------------------------+
-| ``polytrope_mu_e`` | | 2.0e0 |
+| ``polytrope_mu_e`` | mean molecular weight per electron for the cases when | 2.0e0 |
+| | polytrope_type is 1 or 2. In that case, we have P = K | |
+| | (rho / mu_e)**gamma | |
+---------------------------------------+---------------------------------------------------------+------------------------------+
@@ -451,11 +459,14 @@ namespace: ``eos``
+---------------------------------------+---------------------------------------------------------+------------------------------+
| parameter | description | default value |
+=======================================+=========================================================+==============================+
-| ``eos_const_c_v`` | | -1.e0 |
+| ``eos_const_c_v`` | specific heat proportionality constant, K, c_v = K | -1.e0 |
+| | rho**m T**(-n) | |
+---------------------------------------+---------------------------------------------------------+------------------------------+
-| ``eos_c_v_exp_m`` | | 0.e0 |
+| ``eos_c_v_exp_m`` | specific heat density exponent, m, c_v = K rho**m | 0.e0 |
+| | T**(-n) | |
+---------------------------------------+---------------------------------------------------------+------------------------------+
-| ``eos_c_v_exp_n`` | | 0.e0 |
+| ``eos_c_v_exp_n`` | specific heat (negative) temperature exponent, n, c_v = | 0.e0 |
+| | K rho**m T**(-n) | |
+---------------------------------------+---------------------------------------------------------+------------------------------+
@@ -469,9 +480,9 @@ namespace: ``eos``
+---------------------------------------+---------------------------------------------------------+------------------------------+
| ``eos_lb`` | | 1.3 |
+---------------------------------------+---------------------------------------------------------+------------------------------+
-| ``eos_e_0`` | | 1.6e11 |
+| ``eos_e_0`` | minimum energy | 1.6e11 |
+---------------------------------------+---------------------------------------------------------+------------------------------+
-| ``eos_rho_0`` | | 2.7 |
+| ``eos_rho_0`` | reference density | 2.7 |
+---------------------------------------+---------------------------------------------------------+------------------------------+
| ``eos_A`` | | 1.8e11 |
+---------------------------------------+---------------------------------------------------------+------------------------------+
@@ -485,7 +496,7 @@ namespace: ``eos``
+---------------------------------------+---------------------------------------------------------+------------------------------+
| ``eos_beta`` | | 5.0 |
+---------------------------------------+---------------------------------------------------------+------------------------------+
-| ``eos_c_v`` | | 7.9e6 |
+| ``eos_c_v`` | specific heat | 7.9e6 |
+---------------------------------------+---------------------------------------------------------+------------------------------+
@@ -511,14 +522,13 @@ namespace: ``integrator``
+---------------------------------------+---------------------------------------------------------+------------------------------+
| ``burner_verbose`` | Should we print out diagnostic output after the solve? | 0 |
+---------------------------------------+---------------------------------------------------------+------------------------------+
-| ``rtol_spec`` | Tolerances for the solver (relative and absolute), for | 1.e-12 |
-| | the species and energy equations. | |
+| ``rtol_spec`` | relative tolerance for species | 1.e-12 |
+---------------------------------------+---------------------------------------------------------+------------------------------+
-| ``rtol_enuc`` | | 1.e-6 |
+| ``rtol_enuc`` | relative tolerance for energy | 1.e-6 |
+---------------------------------------+---------------------------------------------------------+------------------------------+
-| ``atol_spec`` | | 1.e-8 |
+| ``atol_spec`` | absolute tolerance for species | 1.e-8 |
+---------------------------------------+---------------------------------------------------------+------------------------------+
-| ``atol_enuc`` | | 1.e-6 |
+| ``atol_enuc`` | absolute tolerance for energy | 1.e-6 |
+---------------------------------------+---------------------------------------------------------+------------------------------+
| ``renormalize_abundances`` | Whether to renormalize the mass fractions at each step | 0 |
| | in the evolution so that they sum to unity. | |
@@ -556,15 +566,13 @@ namespace: ``integrator``
| ``retry_swap_jacobian`` | do we swap the Jacobian (from analytic to numerical or | 1 |
| | vice versa) on a retry? | |
+---------------------------------------+---------------------------------------------------------+------------------------------+
-| ``retry_rtol_spec`` | Tolerances for the solver (relative and absolute), for | -1 |
-| | the species and energy equations. If set to < 0, then | |
-| | the same value as the first attempt is used. | |
+| ``retry_rtol_spec`` | relative tolerance for species on retry | -1 |
+---------------------------------------+---------------------------------------------------------+------------------------------+
-| ``retry_rtol_enuc`` | | -1 |
+| ``retry_rtol_enuc`` | relative tolerance for energy on retry | -1 |
+---------------------------------------+---------------------------------------------------------+------------------------------+
-| ``retry_atol_spec`` | | -1 |
+| ``retry_atol_spec`` | absolute tolerance for species on retry | -1 |
+---------------------------------------+---------------------------------------------------------+------------------------------+
-| ``retry_atol_enuc`` | | -1 |
+| ``retry_atol_enuc`` | absolute tolerance for energy on retry | -1 |
+---------------------------------------+---------------------------------------------------------+------------------------------+
| ``do_species_clip`` | in the clean_state process, do we clip the species such | 1 |
| | that they are in [0, 1]? | |
@@ -767,7 +775,7 @@ namespace: ``network``
-**NETWORK_DIR=he-burn.bak/he-burn-18a:**
+**NETWORK_DIR=he-burn/he-burn-18a:**
+---------------------------------------+---------------------------------------------------------+------------------------------+
| parameter | description | default value |
@@ -779,7 +787,7 @@ namespace: ``network``
-**NETWORK_DIR=he-burn.bak/he-burn-22a:**
+**NETWORK_DIR=he-burn/he-burn-22a:**
+---------------------------------------+---------------------------------------------------------+------------------------------+
| parameter | description | default value |
@@ -856,30 +864,6 @@ namespace: ``network``
-**NETWORK_DIR=subch_base:**
-
-+---------------------------------------+---------------------------------------------------------+------------------------------+
-| parameter | description | default value |
-+=======================================+=========================================================+==============================+
-| ``disable_p_C12_to_N13`` | | 0 |
-+---------------------------------------+---------------------------------------------------------+------------------------------+
-| ``disable_He4_N13_to_p_O16`` | | 0 |
-+---------------------------------------+---------------------------------------------------------+------------------------------+
-
-
-
-**NETWORK_DIR=subch_simple:**
-
-+---------------------------------------+---------------------------------------------------------+------------------------------+
-| parameter | description | default value |
-+=======================================+=========================================================+==============================+
-| ``disable_p_C12_to_N13`` | | 0 |
-+---------------------------------------+---------------------------------------------------------+------------------------------+
-| ``disable_He4_N13_to_p_O16`` | | 0 |
-+---------------------------------------+---------------------------------------------------------+------------------------------+
-
-
-
namespace: ``nse``
------------------
@@ -921,7 +905,7 @@ namespace: ``nse``
namespace: ``opacity``
----------------------
-**opacity/rad_power_law:**
+**OPACITY_DIR=rad_power_law:**
+---------------------------------------+---------------------------------------------------------+------------------------------+
| parameter | description | default value |
@@ -1555,8 +1539,6 @@ namespace: ``unit_test``
+---------------------------------------+---------------------------------------------------------+------------------------------+
| ``small_dens`` | | 1.e5 |
+---------------------------------------+---------------------------------------------------------+------------------------------+
-| ``do_acc`` | | 1 |
-+---------------------------------------+---------------------------------------------------------+------------------------------+
@@ -1767,8 +1749,6 @@ namespace: ``unit_test``
+---------------------------------------+---------------------------------------------------------+------------------------------+
| ``small_dens`` | | 1.e5 |
+---------------------------------------+---------------------------------------------------------+------------------------------+
-| ``do_acc`` | | 1 |
-+---------------------------------------+---------------------------------------------------------+------------------------------+
@@ -1831,7 +1811,7 @@ namespace: ``unit_test``
+---------------------------------------+---------------------------------------------------------+------------------------------+
| ``temp_max`` | | 1.e15 |
+---------------------------------------+---------------------------------------------------------+------------------------------+
-| ``uniform_xn`` | | 0 |
+| ``uniform_xn`` | uniform composition | 0 |
+---------------------------------------+---------------------------------------------------------+------------------------------+
| ``tmax`` | | 0.1e0 |
+---------------------------------------+---------------------------------------------------------+------------------------------+
@@ -1839,8 +1819,6 @@ namespace: ``unit_test``
+---------------------------------------+---------------------------------------------------------+------------------------------+
| ``small_dens`` | | 1.e3 |
+---------------------------------------+---------------------------------------------------------+------------------------------+
-| ``do_acc`` | | 1 |
-+---------------------------------------+---------------------------------------------------------+------------------------------+