Merge branch 'development' into reorg_he_nets

AMReX-Astro · Jan 6, 2025 · a7daf58 · a7daf58
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diff --git a/.github/workflows/docs-test.yml b/.github/workflows/docs-test.yml
@@ -35,10 +35,10 @@ jobs:
 
       - name: Build docs
         run: |
-          cd sphinx_docs/
+          cd Docs/
           make SPHINXOPTS='-v -W --keep-going' html
 
       - name: Link check
         run: |
-          cd sphinx_docs/
+          cd Docs/
           make SPHINXOPTS=-v linkcheck
diff --git a/.gitignore b/.gitignore
@@ -78,7 +78,7 @@ extern.f90
 # sphinx
 build/
 doxy_files
-sphinx_docs/source/runtime_parameters.rst
+Docs/source/runtime_parameters.rst
 
 
 # C++ parameters

diff --git a/sphinx_docs/Doxyfile → Docs/Doxyfile b/sphinx_docs/Doxyfile → Docs/Doxyfile
diff --git a/sphinx_docs/Makefile → Docs/Makefile b/sphinx_docs/Makefile → Docs/Makefile
diff --git a/sphinx_docs/converting_docs.txt → Docs/converting_docs.txt b/sphinx_docs/converting_docs.txt → Docs/converting_docs.txt
diff --git a/sphinx_docs/notes.txt → Docs/notes.txt b/sphinx_docs/notes.txt → Docs/notes.txt
diff --git a/sphinx_docs/pandoc.sh → Docs/pandoc.sh b/sphinx_docs/pandoc.sh → Docs/pandoc.sh
diff --git a/sphinx_docs/rp.py → Docs/rp.py b/sphinx_docs/rp.py → Docs/rp.py
diff --git a/sphinx_docs/source/CNO_He_burn.png → Docs/source/CNO_He_burn.png b/sphinx_docs/source/CNO_He_burn.png → Docs/source/CNO_He_burn.png
diff --git a/sphinx_docs/source/ECSN.png → Docs/source/ECSN.png b/sphinx_docs/source/ECSN.png → Docs/source/ECSN.png
diff --git a/...x_docs/source/_static/theme_overrides.css → Docs/source/_static/theme_overrides.css b/...x_docs/source/_static/theme_overrides.css → Docs/source/_static/theme_overrides.css
diff --git a/...nx_docs/source/_templates/dev_layout.html → Docs/source/_templates/dev_layout.html b/...nx_docs/source/_templates/dev_layout.html → Docs/source/_templates/dev_layout.html
diff --git a/sphinx_docs/source/_templates/layout.html → Docs/source/_templates/layout.html b/sphinx_docs/source/_templates/layout.html → Docs/source/_templates/layout.html
diff --git a/sphinx_docs/source/autodiff.rst → Docs/source/autodiff.rst b/sphinx_docs/source/autodiff.rst → Docs/source/autodiff.rst
diff --git a/sphinx_docs/source/cno_extras_hide_alpha.png → Docs/source/cno_extras_hide_alpha.png b/sphinx_docs/source/cno_extras_hide_alpha.png → Docs/source/cno_extras_hide_alpha.png
diff --git a/sphinx_docs/source/comprehensive_tests.rst → Docs/source/comprehensive_tests.rst b/sphinx_docs/source/comprehensive_tests.rst → Docs/source/comprehensive_tests.rst
diff --git a/sphinx_docs/source/conf.py → Docs/source/conf.py b/sphinx_docs/source/conf.py → Docs/source/conf.py
diff --git a/sphinx_docs/source/data_structures.rst → Docs/source/data_structures.rst b/sphinx_docs/source/data_structures.rst → Docs/source/data_structures.rst
diff --git a/sphinx_docs/source/design.rst → Docs/source/design.rst b/sphinx_docs/source/design.rst → Docs/source/design.rst
@@ -12,6 +12,8 @@ and the generic solvers:
 
 * ``constants``: fundamental constants
 
+* ``Docs``: the sphinx source for this documentation
+
 * ``EOS/``: the various equations of state
 
 * ``integration/``: the ODE integration routines used for the
@@ -34,8 +36,6 @@ and the generic solvers:
 * ``screening/``: common electron screening factors used by some of the
   reaction networks.
 
-* ``sphinx_docs``: the sphinx source for this documentation
-
 * ``unit_test/``: self-contained unit tests for Microphysics. These don’t
   need any application code to build, but will require AMReX.
 

diff --git a/sphinx_docs/source/doxygen_network.png → Docs/source/doxygen_network.png b/sphinx_docs/source/doxygen_network.png → Docs/source/doxygen_network.png
diff --git a/sphinx_docs/source/eos.rst → Docs/source/eos.rst b/sphinx_docs/source/eos.rst → Docs/source/eos.rst
diff --git a/sphinx_docs/source/getting_started.rst → Docs/source/getting_started.rst b/sphinx_docs/source/getting_started.rst → Docs/source/getting_started.rst
diff --git a/sphinx_docs/source/index.rst → Docs/source/index.rst b/sphinx_docs/source/index.rst → Docs/source/index.rst
diff --git a/sphinx_docs/source/integrators.rst → Docs/source/integrators.rst b/sphinx_docs/source/integrators.rst → Docs/source/integrators.rst
diff --git a/sphinx_docs/source/mathsymbols.tex → Docs/source/mathsymbols.tex b/sphinx_docs/source/mathsymbols.tex → Docs/source/mathsymbols.tex
diff --git a/sphinx_docs/source/networks-overview.rst → Docs/source/networks-overview.rst b/sphinx_docs/source/networks-overview.rst → Docs/source/networks-overview.rst
diff --git a/sphinx_docs/source/networks.rst → Docs/source/networks.rst b/sphinx_docs/source/networks.rst → Docs/source/networks.rst
diff --git a/sphinx_docs/source/nova.png → Docs/source/nova.png b/sphinx_docs/source/nova.png → Docs/source/nova.png
diff --git a/sphinx_docs/source/nova2.png → Docs/source/nova2.png b/sphinx_docs/source/nova2.png → Docs/source/nova2.png
diff --git a/sphinx_docs/source/nse.rst → Docs/source/nse.rst b/sphinx_docs/source/nse.rst → Docs/source/nse.rst
diff --git a/sphinx_docs/source/ode_integrators.rst → Docs/source/ode_integrators.rst b/sphinx_docs/source/ode_integrators.rst → Docs/source/ode_integrators.rst
diff --git a/sphinx_docs/source/one_zone_tests.rst → Docs/source/one_zone_tests.rst b/sphinx_docs/source/one_zone_tests.rst → Docs/source/one_zone_tests.rst
diff --git a/sphinx_docs/source/react_aprox13_logX.png → Docs/source/react_aprox13_logX.png b/sphinx_docs/source/react_aprox13_logX.png → Docs/source/react_aprox13_logX.png
diff --git a/sphinx_docs/source/refs.bib → Docs/source/refs.bib b/sphinx_docs/source/refs.bib → Docs/source/refs.bib
@@ -626,6 +626,21 @@ @misc{autodiff
     year = {2018}
 }
 
+@ARTICLE{timmes:2000b,
+       author = {{Timmes}, F.~X.},
+        title = "{Physical Properties of Laminar Helium Deflagrations}",
+      journal = {APJ},
+     keywords = {HYDRODYNAMICS, METHODS: NUMERICAL, NUCLEAR REACTIONS, NUCLEOSYNTHESIS, ABUNDANCES, STARS: INTERIORS, Hydrodynamics, Methods: Numerical, nuclear reactions, nucleosynthesis; abundances, Stars: Interiors},
+         year = 2000,
+        month = jan,
+       volume = {528},
+       number = {2},
+        pages = {913-945},
+          doi = {10.1086/308203},
+       adsurl = {https://ui.adsabs.harvard.edu/abs/2000ApJ...528..913T},
+      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
 
 @article{sdc-nse,
 doi = {10.3847/1538-4357/ad8a66},
@@ -671,4 +686,5 @@ @article{langanke:2001
 doi = {https://doi.org/10.1006/adnd.2001.0865},
 author = {K. LANGANKE and G. MARTÍNEZ-PINEDO},
 abstract = {The weak interaction rates in stellar environments are computed for pf-shell nuclei in the mass range A=45–65 using large-scale shell-model calculations. The calculated capture and decay rates take into consideration the latest experimental energy levels and log ft-values. The rates are tabulated at the same grid points of density and temperature as those used by Fuller, Fowler, and Newman for densities ρY e =10–1011 g/cm3 and temperatures T=107–1011 K, and hence are relevant for both types of supernovae (Type Ia and Type II). Effective 〈ft〉 values for capture rates and average neutrino (antineutrino) energies are also given to facilitate the use of interpolated rates in stellar evolution codes.}
-}
+}
+
diff --git a/sphinx_docs/source/rp_intro.rst → Docs/source/rp_intro.rst b/sphinx_docs/source/rp_intro.rst → Docs/source/rp_intro.rst
diff --git a/Docs/source/runtime_parameters.rst b/Docs/source/runtime_parameters.rst
diff --git a/sphinx_docs/source/screening.rst → Docs/source/screening.rst b/sphinx_docs/source/screening.rst → Docs/source/screening.rst
diff --git a/sphinx_docs/source/sdc.rst → Docs/source/sdc.rst b/sphinx_docs/source/sdc.rst → Docs/source/sdc.rst
diff --git a/sphinx_docs/source/subch_base.png → Docs/source/subch_base.png b/sphinx_docs/source/subch_base.png → Docs/source/subch_base.png
diff --git a/sphinx_docs/source/subch_simple.png → Docs/source/subch_simple.png b/sphinx_docs/source/subch_simple.png → Docs/source/subch_simple.png
diff --git a/sphinx_docs/source/templated_networks.rst → Docs/source/templated_networks.rst b/sphinx_docs/source/templated_networks.rst → Docs/source/templated_networks.rst
diff --git a/sphinx_docs/source/tolerances.png → Docs/source/tolerances.png b/sphinx_docs/source/tolerances.png → Docs/source/tolerances.png
diff --git a/Docs/source/transport.rst b/Docs/source/transport.rst
@@ -0,0 +1,134 @@
+**********************
+Transport Coefficients
+**********************
+
+Thermal Conductivity
+====================
+
+The thermal conductivities, $k_\mathrm{th}$, are provided to allow for
+modeling of thermal diffusion, for instance in an energy equation:
+
+.. math::
+
+   \frac{\partial (\rho e)}{\partial t} = \nabla \cdot k_\mathrm{th} \nabla T
+
+Thermal conductivities are provided by the ``conductivity/``
+directory.  The main interface has the form:
+
+.. code:: c++
+
+   template <typename T>
+   AMREX_GPU_HOST_DEVICE AMREX_FORCE_INLINE
+   void conductivity (T& state)
+
+where currently, the input type needs to be the full EOS type, ``eos_t``.  The conductivity
+is then available as ``eos_t eos_state.conductivity``.
+
+.. important::
+
+   It is assumed that the state is thermodynamically consistent
+   before calling the conductivity routine.
+   It may be necessary to do an EOS
+   call first, to enforce the consistency.
+
+There are several implementations of the conductivity currently:
+
+* ``constant`` :
+
+  This simply sets the conductivity to a constant value set via
+  ``conductivity.const_conductivity``.
+
+* ``constant_opacity`` :
+
+  This is intended for creating a conductivity from an opacity, for
+  instance, electron scattering.  The opacity is taken as constant
+  and set via ``conductivity.const_opacity``, and then the conductivity
+  is set as:
+
+  .. math::
+
+     k_\mathrm{th} = \frac{16 \sigma_\mathrm{SB} T^3}{3 \kappa \rho}
+
+  where $\sigma_\mathrm{SB}$ is the Stefan-Boltzmann constant.
+
+* ``powerlaw`` :
+
+  This models a temperature-dependent conductivity of the form:
+
+  .. math::
+
+     k_\mathrm{th} = k_0 T^\nu
+
+  where $k_0$ is set via ``conductivity.cond_coeff`` and $\nu$ is set via
+  ``conductivity.cond_exponent``.
+
+* ``stellar`` :
+
+  This is a general stellar conductivity based on :cite:`timmes:2000b`.
+  It combines radiative opacities and thermal conductivities into a
+  single expression.  This conductivity is suitable for modeling
+  laminar flames.
+
+.. index:: CONDUCTIVITY_DIR
+
+These can be set via the ``CONDUCTIVITY_DIR`` make variable.
+
+
+Radiation Opacities
+===================
+
+For radiation transport, we provide simple opacity routines that return
+the Planck and Rosseland mean opacities.
+
+The interface for these opacities is:
+
+.. code:: c++
+
+   AMREX_GPU_HOST_DEVICE AMREX_INLINE
+   void actual_opacity (Real& kp, Real& kr, Real rho, Real temp, Real rhoYe, Real nu,
+                        bool get_Planck_mean, bool get_Rosseland_mean)
+
+where the boolean ``get_Planck_mean`` and ``get_Rosseland_mean`` specify where those
+opacity terms are filled upon return.
+
+There are 2 interfaces, which are selected via the make variable ``OPACITY_DIR``.
+
+* ``breakout`` :
+
+  This returns a simple electron scattering opacity with a crude approximation
+  connecting the Planck and Rosseland means.
+
+* ``rad_power_law`` :
+
+  This constructs a power-law opacity.  For the Planck mean, it is:
+
+  .. math::
+
+     \kappa_p = \kappa_{p,0} \rho^{m_p} T^{-{n_p}} \nu^{p_p}
+
+  where $\kappa_{p,0}$ is set via ``opacity.const_kappa_p``, $m_p$ is set via ``opacity.kappa_p_exp_m``,
+  $n_p$ is set via ``opacity.kappa_p_exp_n``, and $p_p$ is set via ``opacity.kappa_p_exp_p``.
+
+  The Rosseland mean has a scattering component, $\kappa_s$, which is computed as:
+
+  .. math::
+
+     \kappa_s = \kappa_{s,0} \rho^{m_s} T^{-{n_s}} \nu^{p_s}
+
+  where $\kappa_{s,0}$ is set via ``opacity.const_scatter``, $m_s$ is set via ``opacity.scatter_exp_m``,
+  $n_s$ is set via ``opacity.scatter_n``, and $p_s$ is set via ``opacity.scatter_p``.  The Rosseland
+  mean is then computed as:
+
+  .. math::
+
+     \kappa'_r = \kappa_{r,0} \rho^{m_r} T^{-{n_r}} \nu^{p_r}
+
+  where $\kappa_{r,0}$ is set via ``opacity.const_kappa_r``, $m_r$ is set via ``opacity.kappa_r_exp_m``,
+  $n_r$ is set via ``opacity.kappa_r_exp_n``, and $p_r$ is set via ``opacity.kappa_r_exp_p``, and then
+  combined with scattering as:
+
+  .. math::
+
+     \kappa_r = \max \{ \kappa'_r + \kappa_s, \kappa_\mathrm{floor} \}
+
+  where $\kappa_\mathrm{floor}$ is set via ``opacity.kappa_floor``,
diff --git a/sphinx_docs/source/unit_tests.rst → Docs/source/unit_tests.rst b/sphinx_docs/source/unit_tests.rst → Docs/source/unit_tests.rst
diff --git a/sphinx_docs/source/zreferences.rst → Docs/source/zreferences.rst b/sphinx_docs/source/zreferences.rst → Docs/source/zreferences.rst
diff --git a/sphinx_docs/textsymbols.tex → Docs/textsymbols.tex b/sphinx_docs/textsymbols.tex → Docs/textsymbols.tex
diff --git a/README.md b/README.md
@@ -2,7 +2,9 @@
 
 # Microphysics
 
-*A collection of astrophysical microphysics routines for stellar explosions and interstellar medium chemistry (including primordial chemistry)*
+*A collection of astrophysical microphysics routines for stellar
+explosions and interstellar medium chemistry (including primordial
+chemistry)*
 
 There are several core types of microphysics routines hosted here:
 
@@ -87,7 +89,7 @@ system to ensure the interfaces are tested.
 A user's guide for Microphysics is available at:
 http://amrex-astro.github.io/Microphysics/docs/
 
-The sphinx source for the documentation is in `Microphysics/sphinx_docs/`
+The Sphinx source for the documentation is in `Microphysics/Docs/`
 
 ## Development Model:
 

diff --git a/deploy_docs_action.sh b/deploy_docs_action.sh
@@ -12,19 +12,19 @@ mkdir out
 # if on the dev branch, use the dev_layout.html template to get the
 # links correct
 if [ "$GITHUB_BRANCH" = "$DEV_BRANCH" ]; then
-    mv sphinx_docs/source/_templates/dev_layout.html sphinx_docs/source/_templates/layout.html
+    mv Docs/source/_templates/dev_layout.html Docs/source/_templates/layout.html
 fi
 
 # Build the Sphinx documentation
-cd sphinx_docs
+cd Docs
 make html
 cd ../
 
 mkdir -p out/docs/
 if [ "$GITHUB_BRANCH" = "$MAIN_BRANCH" ]; then
     mkdir -p out/docs
-    mv sphinx_docs/build/html/* out/docs
+    mv Docs/build/html/* out/docs
 else
     mkdir -p out/docs/dev/
-    mv sphinx_docs/build/html/* out/docs/dev
+    mv Docs/build/html/* out/docs/dev
 fi
diff --git a/sphinx_docs/source/transport.rst b/sphinx_docs/source/transport.rst