From 1753bb908e2a966e66a3a79872f4c496c1df9fd3 Mon Sep 17 00:00:00 2001
From: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri, 1 Nov 2024 07:26:31 -0400
Subject: [PATCH 01/13] add changes for 24.11

---
 CHANGES.md | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/CHANGES.md b/CHANGES.md
index 18872f398..ab4a27674 100644
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -1,3 +1,11 @@
+# 24.11
+
+  * a new metal chemistry network was added (#1648, #1650, #1651)
+
+  * add dust temperature to primordial chem (#1649)
+
+  * documentation updates (#1652)
+
 # 24.10
 
   * metal chemistry updates (#1648) with ices (#1650) and cosmic rays (#1651)

From ed9c7fb5de059272644172838258792cbcf684fb Mon Sep 17 00:00:00 2001
From: Ben Wibking <wibkingb@msu.edu>
Date: Thu, 14 Nov 2024 11:38:49 -0500
Subject: [PATCH 02/13] Fix macOS CI (#1666)

---
 .github/workflows/macos_build_cell_metal_chem.yml      | 1 -
 .github/workflows/macos_build_cell_primordial_chem.yml | 1 -
 2 files changed, 2 deletions(-)

diff --git a/.github/workflows/macos_build_cell_metal_chem.yml b/.github/workflows/macos_build_cell_metal_chem.yml
index 581fdd82a..3758f43ca 100644
--- a/.github/workflows/macos_build_cell_metal_chem.yml
+++ b/.github/workflows/macos_build_cell_metal_chem.yml
@@ -12,7 +12,6 @@ jobs:
       - name: Install dependencies
         run: |
           brew install cmake openmpi python3 || true
-          brew link --overwrite python@3.11
 
       - name: Compile and run
         run: |
diff --git a/.github/workflows/macos_build_cell_primordial_chem.yml b/.github/workflows/macos_build_cell_primordial_chem.yml
index 243dae2a4..3e7698432 100644
--- a/.github/workflows/macos_build_cell_primordial_chem.yml
+++ b/.github/workflows/macos_build_cell_primordial_chem.yml
@@ -12,7 +12,6 @@ jobs:
       - name: Install dependencies
         run: |
           brew install cmake openmpi python3 || true
-          brew link --overwrite python@3.11
 
       - name: Compile and run
         run: |

From 8cb64e746c3cf52743439065ba5e922b995b1718 Mon Sep 17 00:00:00 2001
From: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed, 20 Nov 2024 14:47:34 -0500
Subject: [PATCH 03/13] fix linkcheck (#1671)

phys rev does not play nicely
---
 sphinx_docs/source/conf.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/sphinx_docs/source/conf.py b/sphinx_docs/source/conf.py
index a266702ff..64e5ef03d 100644
--- a/sphinx_docs/source/conf.py
+++ b/sphinx_docs/source/conf.py
@@ -223,8 +223,11 @@ def get_version():
 
 linkcheck_retries = 3
 linkcheck_timeout = 100
+linkcheck_allow_unauthorized = True
+linkcheck_ignore = [r"https://doi.org/10.1103/[Pp]hys[Rr]ev*"]
 user_agent = "Mozilla/5.0 (X11; Linux x86_64; rv:25.0) Gecko/20100101 Firefox/25.0"
 
+
 # -- Options for Texinfo output -------------------------------------------
 
 # Grouping the document tree into Texinfo files. List of tuples

From b8767267d28ec7502bd0fc0f08ae955117c7f350 Mon Sep 17 00:00:00 2001
From: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri, 22 Nov 2024 14:25:58 -0500
Subject: [PATCH 04/13] add CI for test_partition_functions (#1673)

---
 .../workflows/test_partition_functions.yml    | 44 +++++++++++++++++++
 .../ci-benchmarks/part_func.out               |  9 ++++
 2 files changed, 53 insertions(+)
 create mode 100644 .github/workflows/test_partition_functions.yml
 create mode 100644 unit_test/test_part_func/ci-benchmarks/part_func.out

diff --git a/.github/workflows/test_partition_functions.yml b/.github/workflows/test_partition_functions.yml
new file mode 100644
index 000000000..275292061
--- /dev/null
+++ b/.github/workflows/test_partition_functions.yml
@@ -0,0 +1,44 @@
+name: test_partition_functions
+
+on: [pull_request]
+jobs:
+  test_partition_functions:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Get AMReX
+        run: |
+          mkdir external
+          cd external
+          git clone https://github.com/AMReX-Codes/amrex.git
+          cd amrex
+          git checkout development
+          echo 'AMREX_HOME=$(GITHUB_WORKSPACE)/external/amrex' >> $GITHUB_ENV
+          echo $AMREX_HOME
+          if [[ -n "${AMREX_HOME}" ]]; then exit 1; fi
+          cd ../..
+
+      - name: Install dependencies
+        run: |
+          sudo apt-get update -y -qq
+          sudo apt-get -qq -y install curl cmake jq clang g++>=9.3.0
+
+      - name: Compile
+        run: |
+          cd unit_test/test_part_func
+          make clean
+          make -j 4
+
+      - name: Run test_part_func
+        run: |
+          cd unit_test/test_part_func
+          ./main3d.gnu.ex > test.out
+
+      - name: Compare to stored output
+        run: |
+          cd unit_test/test_part_func
+          diff -I "^Initializing AMReX" -I "^AMReX" -I "^reading in reaclib rates" test.out ci-benchmarks/part_func.out
+
diff --git a/unit_test/test_part_func/ci-benchmarks/part_func.out b/unit_test/test_part_func/ci-benchmarks/part_func.out
new file mode 100644
index 000000000..6bb827da0
--- /dev/null
+++ b/unit_test/test_part_func/ci-benchmarks/part_func.out
@@ -0,0 +1,9 @@
+Initializing AMReX (24.10-20-gb9d549bcf4a6)...
+AMReX (24.10-20-gb9d549bcf4a6) initialized
+starting the single zone burn...
+reading in network electron-capture / beta-decay tables...
+temperature = 5000000000
+Ni56: 1.010868 2.337172328e-11
+Fe52: 1.743116 3.226066771e-10
+spins: 2 1 1 8 1
+AMReX (24.10-20-gb9d549bcf4a6) finalized

From abec47aecac3227fcbf59272054ed523277d21af Mon Sep 17 00:00:00 2001
From: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon, 25 Nov 2024 11:01:25 -0500
Subject: [PATCH 05/13] remove a stray comment in the subch nets (#1661)

---
 networks/subch_base/subch_base.py     | 3 ---
 networks/subch_simple/subch_simple.py | 3 ---
 2 files changed, 6 deletions(-)

diff --git a/networks/subch_base/subch_base.py b/networks/subch_base/subch_base.py
index b191b3321..af388f856 100644
--- a/networks/subch_base/subch_base.py
+++ b/networks/subch_base/subch_base.py
@@ -94,9 +94,6 @@ def doit():
     net.make_ap_pg_approx(intermediate_nuclei=["cl35", "k39", "sc43", "v47", "mn51", "co55"])
     net.remove_nuclei(["cl35", "k39", "sc43", "v47", "mn51", "co55"])
 
-    # finally, the aprox nets don't include the reverse rates for
-    # C12+C12, C12+O16, and O16+O16, so remove those
-
     print(f"number of nuclei: {len(net.unique_nuclei)}")
     print(f"number of rates: {len(net.rates)}")
 
diff --git a/networks/subch_simple/subch_simple.py b/networks/subch_simple/subch_simple.py
index a4edaa0fe..1983ab455 100644
--- a/networks/subch_simple/subch_simple.py
+++ b/networks/subch_simple/subch_simple.py
@@ -91,9 +91,6 @@ def doit():
     net.make_ap_pg_approx(intermediate_nuclei=["cl35", "k39", "sc43", "v47", "mn51", "co55"])
     net.remove_nuclei(["cl35", "k39", "sc43", "v47", "mn51", "co55"])
 
-    # finally, the aprox nets don't include the reverse rates for
-    # C12+C12, C12+O16, and O16+O16, so remove those
-
     print(f"number of nuclei: {len(net.unique_nuclei)}")
     print(f"number of rates: {len(net.rates)}")
 

From fc1cfa496103ceada91840b94bb03ff24cd2553d Mon Sep 17 00:00:00 2001
From: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon, 25 Nov 2024 11:01:40 -0500
Subject: [PATCH 06/13] we can use -j 4 for make in CI (#1674)

---
 .github/workflows/burn_cell_metal_chem.yml             | 2 +-
 .github/workflows/burn_cell_primordial_chem.yml        | 2 +-
 .github/workflows/c-linter.yml                         | 2 +-
 .github/workflows/castro-development.yml               | 4 ++--
 .github/workflows/castro.yml                           | 4 ++--
 .github/workflows/cmake_build_cell_primordial_chem.yml | 2 +-
 .github/workflows/cuda.yml                             | 6 +++---
 .github/workflows/macos_build_cell_metal_chem.yml      | 2 +-
 .github/workflows/macos_build_cell_primordial_chem.yml | 2 +-
 .github/workflows/test_neutrinos.yml                   | 2 +-
 .github/workflows/test_rhs.yml                         | 2 +-
 11 files changed, 15 insertions(+), 15 deletions(-)

diff --git a/.github/workflows/burn_cell_metal_chem.yml b/.github/workflows/burn_cell_metal_chem.yml
index 6c587eebf..13ec5f98e 100644
--- a/.github/workflows/burn_cell_metal_chem.yml
+++ b/.github/workflows/burn_cell_metal_chem.yml
@@ -31,7 +31,7 @@ jobs:
       - name: Compile
         run: |
           cd unit_test/burn_cell_metal_chem
-          make -j 2
+          make -j 4
 
       - name: Run and compare outputs for different Z values, also including cosmic ray ionization
         run: |
diff --git a/.github/workflows/burn_cell_primordial_chem.yml b/.github/workflows/burn_cell_primordial_chem.yml
index 04f04643e..7b2ba7a78 100644
--- a/.github/workflows/burn_cell_primordial_chem.yml
+++ b/.github/workflows/burn_cell_primordial_chem.yml
@@ -31,7 +31,7 @@ jobs:
       - name: Compile and run
         run: |
           cd unit_test/burn_cell_primordial_chem
-          make -j 2
+          make -j 4
           ./main1d.gnu.DEBUG.ex inputs_primordial_chem amrex.fpe_trap_{invalid,zero,overflow}=1 > test.out
 
       - name: Print backtrace
diff --git a/.github/workflows/c-linter.yml b/.github/workflows/c-linter.yml
index 56d6bc723..30e4baa8c 100644
--- a/.github/workflows/c-linter.yml
+++ b/.github/workflows/c-linter.yml
@@ -26,7 +26,7 @@ jobs:
         uses: AMReX-Astro/cpp-linter-action@main
         with:
           build_path: 'unit_test/test_react'
-          make_options: '-j 2 USE_OMP=FALSE USE_MPI=FALSE USE_CUDA=FALSE DEBUG=TRUE'
+          make_options: '-j 4 USE_OMP=FALSE USE_MPI=FALSE USE_CUDA=FALSE DEBUG=TRUE'
           ignore_files: 'amrex|util/gcem'
           header_filter: '(/conductivity/|/constants/|/EOS/|/integration/|/interfaces/|/networks/|/neutrinos/|/nse_solver/|/opacity/|/rates/|/screening/|/util/|^\./).*\.H$'
           config_file: ${GITHUB_WORKSPACE}/.clang-tidy
diff --git a/.github/workflows/castro-development.yml b/.github/workflows/castro-development.yml
index 451f4c203..273e32a7c 100644
--- a/.github/workflows/castro-development.yml
+++ b/.github/workflows/castro-development.yml
@@ -47,7 +47,7 @@ jobs:
         export MICROPHYSICS_HOME=${PWD}
 
         cd Castro/Exec/science/flame_wave/
-        make -j2 CCACHE=ccache USE_MPI=FALSE
+        make -j 4 CCACHE=ccache USE_MPI=FALSE
 
         ccache -s
         du -hs ~/.cache/ccache
@@ -64,7 +64,7 @@ jobs:
         export MICROPHYSICS_HOME=${PWD}
 
         cd Castro/Exec/science/subchandra/
-        make -j2 CCACHE=ccache USE_MPI=FALSE
+        make -j 4 CCACHE=ccache USE_MPI=FALSE
 
         ccache -s
         du -hs ~/.cache/ccache
diff --git a/.github/workflows/castro.yml b/.github/workflows/castro.yml
index 0ea9864ac..4a5b1d58e 100644
--- a/.github/workflows/castro.yml
+++ b/.github/workflows/castro.yml
@@ -51,7 +51,7 @@ jobs:
         export MICROPHYSICS_HOME=${PWD}
 
         cd Castro/Exec/science/flame_wave/
-        make -j2 CCACHE=ccache USE_MPI=FALSE
+        make -j 4 CCACHE=ccache USE_MPI=FALSE
 
         ccache -s
         du -hs ~/.cache/ccache
@@ -68,7 +68,7 @@ jobs:
         export MICROPHYSICS_HOME=${PWD}
 
         cd Castro/Exec/science/subchandra/
-        make -j2 CCACHE=ccache USE_MPI=FALSE
+        make -j 4 CCACHE=ccache USE_MPI=FALSE
 
         ccache -s
         du -hs ~/.cache/ccache
diff --git a/.github/workflows/cmake_build_cell_primordial_chem.yml b/.github/workflows/cmake_build_cell_primordial_chem.yml
index 844ab4c8d..606377072 100644
--- a/.github/workflows/cmake_build_cell_primordial_chem.yml
+++ b/.github/workflows/cmake_build_cell_primordial_chem.yml
@@ -18,5 +18,5 @@ jobs:
         run: |
           mkdir build && cd build
           cmake .. -DBUILD_UNIT_TEST=true -DBUILD_AMReX=true
-          make -j2
+          make -j 4
           ctest --output-on-failure
diff --git a/.github/workflows/cuda.yml b/.github/workflows/cuda.yml
index 7e418249a..fab16b93f 100644
--- a/.github/workflows/cuda.yml
+++ b/.github/workflows/cuda.yml
@@ -32,17 +32,17 @@ jobs:
         run: |
           export PATH=/usr/local/nvidia/bin:/usr/local/cuda/bin:${PATH}
           cd unit_test/test_react
-          make NETWORK_DIR=aprox13 USE_CUDA=TRUE COMP=gnu USE_MPI=FALSE -j 2
+          make NETWORK_DIR=aprox13 USE_CUDA=TRUE COMP=gnu USE_MPI=FALSE -j 4
 
       - name: compile test_react (ignition_reaclib/URCA-simple)
         run: |
           export PATH=/usr/local/nvidia/bin:/usr/local/cuda/bin:${PATH}
           cd unit_test/test_react
           make realclean
-          make NETWORK_DIR=ignition_reaclib/URCA-simple USE_CUDA=TRUE COMP=gnu USE_MPI=FALSE -j 2
+          make NETWORK_DIR=ignition_reaclib/URCA-simple USE_CUDA=TRUE COMP=gnu USE_MPI=FALSE -j 4
 
       - name: compile test_nse_net (ase)
         run: |
           export PATH=/usr/local/nvidia/bin:/usr/local/cuda/bin:${PATH}
           cd unit_test/test_nse_net
-          make USE_CUDA=TRUE COMP=gnu USE_MPI=FALSE -j 2
+          make USE_CUDA=TRUE COMP=gnu USE_MPI=FALSE -j 4
diff --git a/.github/workflows/macos_build_cell_metal_chem.yml b/.github/workflows/macos_build_cell_metal_chem.yml
index 3758f43ca..7880dabaf 100644
--- a/.github/workflows/macos_build_cell_metal_chem.yml
+++ b/.github/workflows/macos_build_cell_metal_chem.yml
@@ -17,5 +17,5 @@ jobs:
         run: |
           mkdir build && cd build
           cmake .. -DBUILD_UNIT_TEST_MC=true -DBUILD_AMReX=true
-          make -j2
+          make -j 4
           ctest --output-on-failure
diff --git a/.github/workflows/macos_build_cell_primordial_chem.yml b/.github/workflows/macos_build_cell_primordial_chem.yml
index 3e7698432..0390c426c 100644
--- a/.github/workflows/macos_build_cell_primordial_chem.yml
+++ b/.github/workflows/macos_build_cell_primordial_chem.yml
@@ -17,5 +17,5 @@ jobs:
         run: |
           mkdir build && cd build
           cmake .. -DBUILD_UNIT_TEST_PC=true -DBUILD_AMReX=true
-          make -j2
+          make -j 4
           ctest --output-on-failure
diff --git a/.github/workflows/test_neutrinos.yml b/.github/workflows/test_neutrinos.yml
index 46cb99cd8..4ab1a80cc 100644
--- a/.github/workflows/test_neutrinos.yml
+++ b/.github/workflows/test_neutrinos.yml
@@ -29,7 +29,7 @@ jobs:
       - name: Build the fextrema tool
         run: |
           cd external/amrex/Tools/Plotfile
-          make programs=fextrema -j 2
+          make programs=fextrema -j 4
 
       - name: Compile
         run: |
diff --git a/.github/workflows/test_rhs.yml b/.github/workflows/test_rhs.yml
index 465420051..21b4a9dcd 100644
--- a/.github/workflows/test_rhs.yml
+++ b/.github/workflows/test_rhs.yml
@@ -29,7 +29,7 @@ jobs:
       - name: Build the fextrema tool
         run: |
           cd external/amrex/Tools/Plotfile
-          make programs=fextrema -j 2
+          make programs=fextrema -j 4
 
       - name: Compile, test_rhs (VODE, ignition_simple)
         run: |

From b41ff254a55f20448f92d6aad03b09c5518af056 Mon Sep 17 00:00:00 2001
From: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon, 25 Nov 2024 11:02:05 -0500
Subject: [PATCH 07/13] add a init_species_all_equal option to burn_cell
 (#1665)

if this is True, then we don't need to specify the mass fractions
individually, instead they are all initialized to X = 1/NumSpec
---
 unit_test/burn_cell/GNUmakefile |  2 +-
 unit_test/burn_cell/_parameters |  2 ++
 unit_test/burn_cell/burn_cell.H | 11 +++++++----
 3 files changed, 10 insertions(+), 5 deletions(-)

diff --git a/unit_test/burn_cell/GNUmakefile b/unit_test/burn_cell/GNUmakefile
index 8372650eb..394010020 100644
--- a/unit_test/burn_cell/GNUmakefile
+++ b/unit_test/burn_cell/GNUmakefile
@@ -24,7 +24,7 @@ EOS_DIR     := helmholtz
 
 # This sets the network directory
 NETWORK_DIR := aprox13
-
+SCREEN_METHOD := screen5
 CONDUCTIVITY_DIR := stellar
 
 INTEGRATOR_DIR =  VODE
diff --git a/unit_test/burn_cell/_parameters b/unit_test/burn_cell/_parameters
index 9047a84f8..9dc27e92e 100644
--- a/unit_test/burn_cell/_parameters
+++ b/unit_test/burn_cell/_parameters
@@ -19,3 +19,5 @@ density       real       1.e7
 temperature   real       3.e9
 
 skip_initial_normalization    bool    0
+
+init_species_all_equal        bool    0
diff --git a/unit_test/burn_cell/burn_cell.H b/unit_test/burn_cell/burn_cell.H
index 71f379471..43496f1a6 100644
--- a/unit_test/burn_cell/burn_cell.H
+++ b/unit_test/burn_cell/burn_cell.H
@@ -21,12 +21,15 @@ void burn_cell_c()
     // Make sure user set all the mass fractions to values in the interval [0, 1]
     for (int n = 1; n <= NumSpec; ++n) {
 
-        massfractions[n-1] = get_xn(n);
+        if (unit_test_rp::init_species_all_equal) {
+            massfractions[n-1] = 1.0_rt / static_cast<amrex::Real>(NumSpec);
+        } else {
+            massfractions[n-1] = get_xn(n);
 
-        if (massfractions[n-1] < 0 || massfractions[n-1] > 1) {
-            amrex::Error("mass fraction for " + short_spec_names_cxx[n-1] + " not initialized in the interval [0,1]!");
+            if (massfractions[n-1] < 0 || massfractions[n-1] > 1) {
+                amrex::Error("mass fraction for " + short_spec_names_cxx[n-1] + " not initialized in the interval [0,1]!");
+            }
         }
-
     }
 
     // Echo initial conditions at burn and fill burn state input

From 1ac4c12977d66923b2c051dcfc82ccb76bc47e49 Mon Sep 17 00:00:00 2001
From: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon, 25 Nov 2024 11:02:29 -0500
Subject: [PATCH 08/13] use narrower eos_extra_t variants in the NSE table
 routines (#1668)

this should reduce memory
---
 nse_tabular/nse_eos.H | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/nse_tabular/nse_eos.H b/nse_tabular/nse_eos.H
index 425e0d70d..100688932 100644
--- a/nse_tabular/nse_eos.H
+++ b/nse_tabular/nse_eos.H
@@ -65,7 +65,7 @@ nse_T_abar_from_e(const amrex::Real rho, const amrex::Real e_in, const amrex::Re
         amrex::Real abar_old = nse_state.abar;
 
         // call the EOS with the initial guess for T
-        eos_extra_t eos_state;
+        eos_re_extra_t eos_state;
         eos_state.rho = rho;
         eos_state.T = T;
         eos_state.aux[iye] = Ye;
@@ -156,7 +156,7 @@ nse_rho_abar_from_e(const amrex::Real T, const amrex::Real e_in, const amrex::Re
         amrex::Real abar_old = nse_state.abar;
 
         // call the EOS with the initial guess for rho
-        eos_extra_t eos_state;
+        eos_re_extra_t eos_state;
         eos_state.rho = rho;
         eos_state.T = T;
         eos_state.aux[iye] = Ye;
@@ -247,7 +247,7 @@ nse_T_abar_from_p(const amrex::Real rho, const amrex::Real p_in, const amrex::Re
         amrex::Real abar_old = nse_state.abar;
 
         // call the EOS with the initial guess for T
-        eos_extra_t eos_state;
+        eos_rep_extra_t eos_state;
         eos_state.rho = rho;
         eos_state.T = T;
         eos_state.aux[iye] = Ye;
@@ -338,7 +338,7 @@ nse_rho_abar_from_p(const amrex::Real T, const amrex::Real p_in, const amrex::Re
         amrex::Real abar_old = nse_state.abar;
 
         // call the EOS with the initial guess for rho
-        eos_extra_t eos_state;
+        eos_rep_extra_t eos_state;
         eos_state.rho = rho;
         eos_state.T = T;
         eos_state.aux[iye] = Ye;

From 3ceedde150441c8e902d7da842f4faf8d97d4dfb Mon Sep 17 00:00:00 2001
From: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon, 25 Nov 2024 11:02:54 -0500
Subject: [PATCH 09/13] some clang-tidy 19 fixes (#1664)

---
 .clang-tidy                       |  3 +++
 integration/VODE/vode_dvhin.H     | 10 +++-------
 networks/aprox13/actual_network.H |  2 +-
 networks/aprox21/actual_network.H |  2 +-
 networks/iso7/actual_network.H    |  2 +-
 networks/rprox/actual_network.H   |  2 +-
 6 files changed, 10 insertions(+), 11 deletions(-)

diff --git a/.clang-tidy b/.clang-tidy
index 1e228494a..2bd4310f7 100644
--- a/.clang-tidy
+++ b/.clang-tidy
@@ -19,6 +19,7 @@ Checks: >
        -misc-include-cleaner,
        -misc-non-private-member-variables-in-classes,
        -misc-use-anonymous-namespace,
+       -misc-use-internal-linkage,
      modernize-*,
        -modernize-avoid-c-arrays,
        -modernize-use-trailing-return-type,
@@ -29,12 +30,14 @@ Checks: >
        -readability-avoid-const-params-in-decls,
        -readability-braces-around-statements,
        -readability-else-after-return,
+       -readability-enum-initial-value,
        -readability-function-cognitive-complexity,
        -readability-function-size,
        -readability-identifier-length,
        -readability-implicit-bool-conversion,
        -readability-isolate-declaration,
        -readability-magic-numbers,
+       -readability-math-missing-parentheses,
        -readability-named-parameter,
        -readability-simplify-boolean-expr,
      mpi-*,
diff --git a/integration/VODE/vode_dvhin.H b/integration/VODE/vode_dvhin.H
index 055ddc139..20c674722 100644
--- a/integration/VODE/vode_dvhin.H
+++ b/integration/VODE/vode_dvhin.H
@@ -122,17 +122,13 @@ void dvhin (BurnT& state, DvodeT& vstate, amrex::Real& H0, int& NITER, int& IER)
 
         }
 
-        // Iteration done. Apply bounds, bias factor, and sign. Then exit.
+        // Iteration done. Apply bounds and bias factor. Then exit.
         H0 = hnew * 0.5_rt;
-        if (H0 < HLB) {
-            H0 = HLB;
-        }
-        if (H0 > HUB) {
-            H0 = HUB;
-        }
+        H0 = std::clamp(H0, HLB, HUB);
 
     }
 
+    // apply sign
     H0 = std::copysign(H0, vstate.tout - vstate.t);
     NITER = iter;
     IER = 0;
diff --git a/networks/aprox13/actual_network.H b/networks/aprox13/actual_network.H
index 937585dd8..f67812327 100644
--- a/networks/aprox13/actual_network.H
+++ b/networks/aprox13/actual_network.H
@@ -134,7 +134,7 @@ namespace NSE_INDEX
 #endif
 
 namespace Rates {
-    enum NetworkRates {
+    enum NetworkRates: std::uint8_t {
         He4_He4_He4_to_C12 = 1,
         C12_He4_to_O16,
         C12_C12_to_Ne20_He4,
diff --git a/networks/aprox21/actual_network.H b/networks/aprox21/actual_network.H
index dcade97f0..9fca91944 100644
--- a/networks/aprox21/actual_network.H
+++ b/networks/aprox21/actual_network.H
@@ -152,7 +152,7 @@ namespace NSE_INDEX
 #endif
 
 namespace Rates {
-    enum NetworkRates {
+    enum NetworkRates : std::uint8_t {
         H1_H1_to_He3 = 1,
         H1_H1_H1_to_He3,
         P_to_N,
diff --git a/networks/iso7/actual_network.H b/networks/iso7/actual_network.H
index ea60bd035..82f81313c 100644
--- a/networks/iso7/actual_network.H
+++ b/networks/iso7/actual_network.H
@@ -114,7 +114,7 @@ namespace NSE_INDEX
 #endif
 
 namespace Rates {
-    enum NetworkRates {
+    enum NetworkRates : std::uint8_t {
         C12_He4_to_O16 = 1,
         He4_He4_He4_to_C12,
         C12_C12_to_Ne20_He4,
diff --git a/networks/rprox/actual_network.H b/networks/rprox/actual_network.H
index c16d12dc6..4afd4fc8b 100644
--- a/networks/rprox/actual_network.H
+++ b/networks/rprox/actual_network.H
@@ -112,7 +112,7 @@ namespace network
 
 namespace Rates
 {
-    enum NetworkRates
+    enum NetworkRates : std::uint8_t
     {
         He4_He4_He4_to_C12 = 1,
         C12_H1_to_N13,

From 9d58404bbf0e9d48662ef6406aad81f403a308b6 Mon Sep 17 00:00:00 2001
From: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon, 25 Nov 2024 11:45:45 -0500
Subject: [PATCH 10/13] bump CI up to clang-tidy 19 (#1675)

---
 .github/workflows/clang-tidy.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/clang-tidy.yml b/.github/workflows/clang-tidy.yml
index 6482717f8..6563da5f7 100644
--- a/.github/workflows/clang-tidy.yml
+++ b/.github/workflows/clang-tidy.yml
@@ -26,10 +26,10 @@ jobs:
 
       - name: Install dependencies
         run: |
-          .github/workflows/dependencies_clang-tidy-apt-llvm.sh 17
+          .github/workflows/dependencies_clang-tidy-apt-llvm.sh 19
 
       - name: Compile burn_cell_sdc
         run: |
           cd unit_test/burn_cell_sdc
-          make USE_MPI=FALSE USE_CLANG_TIDY=TRUE CLANG_TIDY=clang-tidy-17 CLANG_TIDY_WARN_ERROR=TRUE -j 4
+          make USE_MPI=FALSE USE_CLANG_TIDY=TRUE CLANG_TIDY=clang-tidy-19 CLANG_TIDY_WARN_ERROR=TRUE -j 4
 

From cfe27ade912a566171b1ab2c564453ec5b95d0cc Mon Sep 17 00:00:00 2001
From: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon, 25 Nov 2024 11:46:16 -0500
Subject: [PATCH 11/13] start of some doc fixes (#1667)

this improves the landing page and eliminates the preface
also remove some old text that is no longer accurate
finally, start working on the index
---
 sphinx_docs/source/data_structures.rst   | 10 ++++-
 sphinx_docs/source/eos.rst               | 55 ++++++++++++++++--------
 sphinx_docs/source/getting_started.rst   |  6 +++
 sphinx_docs/source/index.rst             | 42 +++++++++++++-----
 sphinx_docs/source/integrators.rst       | 14 +++---
 sphinx_docs/source/networks-overview.rst |  8 ++--
 sphinx_docs/source/networks.rst          |  2 +
 sphinx_docs/source/nse.rst               |  2 +
 sphinx_docs/source/one_zone_tests.rst    |  2 +
 sphinx_docs/source/preface.rst           | 30 -------------
 sphinx_docs/source/screening.rst         | 12 +++++-
 sphinx_docs/source/sdc.rst               |  1 +
 sphinx_docs/source/unit_tests.rst        |  6 +++
 13 files changed, 120 insertions(+), 70 deletions(-)
 delete mode 100644 sphinx_docs/source/preface.rst

diff --git a/sphinx_docs/source/data_structures.rst b/sphinx_docs/source/data_structures.rst
index a76cf1f0c..8a4c4ccc3 100644
--- a/sphinx_docs/source/data_structures.rst
+++ b/sphinx_docs/source/data_structures.rst
@@ -13,6 +13,8 @@ EOS
 ``eos_t``
 ---------
 
+.. index:: eos_t
+
 The main data structure for interacting with the EOS is ``eos_t``.
 This is a collection of data specifying the microphysical state of the
 fluid that we are evaluating. This has many components. For a
@@ -49,6 +51,8 @@ Networks
 ``burn_t``
 ----------
 
+.. index:: burn_t
+
 The main data structure for interacting with the reaction networks is
 ``burn_t``. This holds the composition (mass fractions), thermodynamic
 state, and a lot of internal information used by the reaction network
@@ -89,7 +93,9 @@ the user will only need to fill/use the following information:
 ``rate_t``, ``rate_fr_t``
 -------------------------
 
-The ``rate_t`` and ``rate_fr_t`` structures are used internally in a network to pass the
+.. index:: rate_t
+
+The ``rate_t`` structure is used internally in a network to pass the
 raw reaction rate information (usually just the temperature-dependent
 terms) between various subroutines. It does not come out of the
 network-specific righthand side or Jacobian routines.
@@ -97,6 +103,8 @@ network-specific righthand side or Jacobian routines.
 ``burn_type.H``
 ---------------
 
+.. index:: burn_type.H
+
 In addition to defining the ``burn_t`` type, the header ``burn_type.H``
 also defines integer indices into the solution vector that can be used
 to access the different components of the state:
diff --git a/sphinx_docs/source/eos.rst b/sphinx_docs/source/eos.rst
index f49d4987f..dee9ee809 100644
--- a/sphinx_docs/source/eos.rst
+++ b/sphinx_docs/source/eos.rst
@@ -9,6 +9,8 @@ an EOS module in case you want to build your own.
 Available Equations of State
 ============================
 
+.. index:: eos_t
+
 The following equations of state are available in Microphysics.
 Except where noted, each of these EOSs will provide the full
 thermodynamic data (including all derivatives) in the ``eos_t``
@@ -22,7 +24,7 @@ equation of state:
 
 .. math:: p = (\gamma - 1) \rho e.
 
-:math:`\gamma` is specified by the runtime parameter ``eos_gamma``. For
+:math:`\gamma` is specified by the runtime parameter ``eos.eos_gamma``. For
 an ideal gas, this represents the ratio of specific heats. The gas is
 assumed to be ideal, with the pressure given by
 
@@ -30,12 +32,12 @@ assumed to be ideal, with the pressure given by
 
 where :math:`k` is Boltzmann’s constant and :math:`\mu` is the mean molecular
 weight, calculated from the composition, :math:`X_k`. This EOS assumes
-the gas is either completely neutral (``assume_neutral = T``),
+the gas is either completely neutral (``eos.assume_neutral = 1``),
 giving:
 
 .. math:: \mu^{-1} = \sum_k \frac{X_k}{A_k}
 
-or completely ionized (``assume_neutral = F``), giving:
+or completely ionized (``eos.assume_neutral = 0``), giving:
 
 .. math:: \mu^{-1} = \sum_k \left ( 1 + Z_k \right ) \frac{X_k}{A_k}
 
@@ -43,11 +45,6 @@ The entropy comes from the Sackur-Tetrode equation. Because of the
 complex way that composition enters into the entropy, the entropy
 formulation here is only correct for a :math:`\gamma = 5/3` gas.
 
-Note that the implementation provided in Microphysics is the same as
-the version shipped with MAESTRO, but more general than the
-``gamma_law`` EOS provided with CASTRO. CASTRO’s default EOS only
-fills the thermodynamic information in ``eos_t`` that is required
-by the hydrodynamics module in CASTRO.
 
 polytrope
 ---------
@@ -63,21 +60,21 @@ only independent variable; there is no temperature dependence. The
 user either selects from a set of predefined options reflecting
 physical polytropes (e.g. a non-relativistic, fully degenerate
 electron gas) or inputs their own values for :math:`K` and :math:`\gamma`
-via ``polytrope_K`` and ``polytrope_gamma``.
+via ``eos.polytrope_K`` and ``eos.polytrope_gamma``.
 
-The runtime parameter ``polytrope_type`` selects the pre-defined
+The runtime parameter ``eos.polytrope_type`` selects the pre-defined
 polytropic relations. The options are:
 
--  ``polytrope_type = 1``: sets :math:`\gamma = 5/3` and
+-  ``eos.polytrope_type = 1``: sets :math:`\gamma = 5/3` and
 
    .. math:: K = \left ( \frac{3}{\pi} \right)^{2/3} \frac{h^2}{20 m_e m_p^{5/3}} \frac{1}{\mu_e^{5/3}}
 
-   where :math:`mu_e` is the mean molecular weight per electron, specified via ``polytrope_mu_e``
+   where :math:`mu_e` is the mean molecular weight per electron, specified via ``eos.polytrope_mu_e``
 
    This is the form appropriate for a non-relativistic
    fully-degenerate electron gas.
 
--  ``polytrope_type = 2``: sets :math:`\gamma = 4/3` and
+-  ``eos.polytrope_type = 2``: sets :math:`\gamma = 4/3` and
 
    .. math:: K = \left ( \frac{3}{\pi} \right)^{1/3} \frac{hc}{8 m_p^{4/3}} \frac{1}{\mu_e^{4/3}}
 
@@ -161,12 +158,12 @@ and :math:`p = \rho e (\gamma_\mathrm{effective} - 1)`.
 This equation of state takes several runtime parameters that can set
 the :math:`\gamma_i` for a specific species. The parameters are:
 
--  ``eos_gamma_default``: the default :math:`\gamma` to apply for all
+-  ``eos.eos_gamma_default``: the default :math:`\gamma` to apply for all
    species
 
--  ``species_X_name`` and ``species_X_gamma``: set the
+-  ``eos.species_X_name`` and ``eos.species_X_gamma``: set the
    :math:`\gamma_i` for the species whose name is given as
-   ``species_X_name`` to the value provided by ``species_X_gamma``.
+   ``eos.species_X_name`` to the value provided by ``eos.species_X_gamma``.
    Here, ``X`` can be one of the letters: ``a``, ``b``, or
    ``c``, allowing us to specify custom :math:`\gamma_i` for up to three
    different species.
@@ -209,6 +206,8 @@ appropriate interpolation table from that site to use this.
 Interface and Modes
 ===================
 
+.. index:: eos_t, eos_re_t, eos_rep_t, eos_rh_t, chem_eos_t
+
 The EOS is called as:
 
 .. code:: c++
@@ -244,6 +243,11 @@ The *eos_type* passed in is one of
 
 * ``eos_rep_t`` : expands on ``eos_re_t`` to include pressure information
 
+* ``eos_rh_t`` : expands on ``eos_rep_t`` to include enthalpy information
+
+* ``chem_eos_t`` : adds some quantities needed for the primordial chemistry EOS
+  and explicitly does not include the mass fractions.
+
 In general, you should use the type that has the smallest set of
 information needed, since we optimize out needless quantities at
 compile type (via C++ templating) for ``eos_re_t`` and ``eos_rep_t``.
@@ -260,6 +264,7 @@ compile type (via C++ templating) for ``eos_re_t`` and ``eos_rep_t``.
 Auxiliary Composition
 ---------------------
 
+.. index:: USE_AUX_THERMO
 
 With ``USE_AUX_THERMO=TRUE``, we interpret the composition from the auxiliary variables.
 The auxiliary variables are
@@ -298,6 +303,21 @@ The equation of state also needs :math:`\bar{Z}` which is easily computed as
    \bar{Z} = \bar{A} Y_e
 
 
+Composition Derivatives
+-----------------------
+
+.. index:: eos_extra_t, eos_re_extra_t, eos_rep_extra_t
+
+The derivatives $\partial p/\partial A$, $\partial p/\partial Z$,
+and $\partial e/\partial A$, $\partial e/\partial Z$ are available via
+the ``eos_extra_t``, ``eos_re_extra_t``, ``eos_rep_extra_t``, which
+extends the non-"extra" variants with these additional fields.
+
+The composition derivatives can be used via the ``composition_derivatives()`` function
+in ``eos_composition.H``
+to compute :math:`\partial p/\partial X_k |_{\rho, T, X_j}`, :math:`\partial e/\partial X_k |_{\rho, T, X_j}`, and :math:`\partial h/\partial X_k |_{\rho, T, X_j}`.
+
+
 Initialization and Cutoff Values
 ================================
 
@@ -328,6 +348,3 @@ appropriate time for, say, loading an interpolation table into memory.
 
 The main evaluation routine is called ``actual_eos``. It should
 accept an eos_input and an eos_t state; see Section :ref:`data_structures`.
-
-
-
diff --git a/sphinx_docs/source/getting_started.rst b/sphinx_docs/source/getting_started.rst
index a338f28ec..b02c12124 100644
--- a/sphinx_docs/source/getting_started.rst
+++ b/sphinx_docs/source/getting_started.rst
@@ -5,6 +5,8 @@ Getting Started
 Standalone
 ==========
 
+.. index:: AMREX_HOME
+
 Microphysics can be used in a "standalone" fashion to run the unit
 tests and explore the behavior of the reaction networks.  The main
 requirement is a copy of AMReX:
@@ -23,6 +25,8 @@ to set the ``AMREX_HOME`` environment variable to point to the
 
 (where you change ``/path/to/amrex`` to your actual path).
 
+.. index:: burn_cell
+
 A good unit test to start with is ``burn_cell`` -- this is simply a
 one-zone burn.  In ``Microphysics/`` do:
 
@@ -45,6 +49,8 @@ Here ``inputs_aprox21`` is the inputs file that sets options.
 Running with AMReX Application Code
 ===================================
 
+.. index:: MICROPHYSICS_HOME
+
 Getting started with Microphysics using either CASTRO or MAESTROeX is
 straightforward. Because the modules here are already in a format that
 the AMReX codes understand, you only need to provide to the code
diff --git a/sphinx_docs/source/index.rst b/sphinx_docs/source/index.rst
index 7b48af3de..c0e9fc762 100644
--- a/sphinx_docs/source/index.rst
+++ b/sphinx_docs/source/index.rst
@@ -6,18 +6,36 @@
 AMReX-Astro Microphysics
 ************************
 
-A collection of microphysics routines (equations of state,
+AMReX-Astro Microphysics is a collection of microphysics routines (equations of state,
 reaction networks, ...) and utilities (ODE integrators, NSE solvers)
 for astrophysical simulation codes.
 
-.. toctree::
-   :maxdepth: 1
+The original design was to support the `AMReX
+<https://github.com/amrex-codes/amrex>`_ codes `CASTRO
+<https://github.com/amrex-astro/Castro>`_ and MAESTRO (now `MAESTROeX
+<https://github.com/amrex-astro/MAESTROeX>`_). These all have a
+consistent interface and the separate Microphysics repository allows
+them to share the same equation of state, reaction networks, and more.
+Later, Microphysics was adopted by the `Quokka <https://github.com/quokka-astro/quokka>`_
+simulation code.
+
+While there are a number of unit tests that exercise the functionality,
+Microphysics is primarily intended to be used along with another simulation
+code.   At the moment, the interfaces and
+build stubs are compatible with the AMReX codes and use the AMReX build
+system.
+
+A number of the routines contained here we authored by other people.
+We bundle them here with permission, usually changing the interfaces
+to be compatible with our standardized interface. We in particular
+thank Frank Timmes for numerous reaction networks and his equation
+of state routines.
 
-   preface
 
 .. toctree::
    :maxdepth: 1
    :caption: Microphysics overview
+   :hidden:
 
    getting_started
    design
@@ -28,6 +46,7 @@ for astrophysical simulation codes.
 .. toctree::
    :maxdepth: 1
    :caption: EOS and transport
+   :hidden:
 
    eos
    transport
@@ -35,6 +54,7 @@ for astrophysical simulation codes.
 .. toctree::
    :maxdepth: 1
    :caption: Reaction networks
+   :hidden:
 
    networks-overview
    networks
@@ -44,6 +64,7 @@ for astrophysical simulation codes.
 .. toctree::
    :maxdepth: 1
    :caption: ODE integrators
+   :hidden:
 
    integrators
    ode_integrators
@@ -53,6 +74,7 @@ for astrophysical simulation codes.
 .. toctree::
    :maxdepth: 1
    :caption: Unit tests
+   :hidden:
 
    unit_tests
    comprehensive_tests
@@ -61,13 +83,13 @@ for astrophysical simulation codes.
 .. toctree::
    :maxdepth: 1
    :caption: References
+   :hidden:
 
    zreferences
 
+.. toctree::
+   :maxdepth: 1
+   :caption: Index
+   :hidden:
 
-Indices and tables
-==================
-
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`
+   genindex
diff --git a/sphinx_docs/source/integrators.rst b/sphinx_docs/source/integrators.rst
index cf6c87565..77c6b9306 100644
--- a/sphinx_docs/source/integrators.rst
+++ b/sphinx_docs/source/integrators.rst
@@ -17,11 +17,13 @@ The equations we integrate to do a nuclear burn are:
    \frac{de}{dt} = f(\rho,X_k,T)
    :label: eq:enuc_integrate
 
-Here, :math:`X_k` is the mass fraction of species :math:`k`, :math:`e` is the specific
-nuclear energy created through reactions. Also needed are density :math:`\rho`,
-temperature :math:`T`, and the specific heat. The function :math:`f` provides the energy release from reactions and can often be expressed in terms of the
-instantaneous reaction terms, :math:`\dot{X}_k`. As noted in the previous
-section, this is implemented in a network-specific manner.
+Here, :math:`X_k` is the mass fraction of species :math:`k`, :math:`e`
+is the specific nuclear energy created through reactions. Also needed
+are density :math:`\rho`, temperature :math:`T`, and the specific
+heat. The function :math:`f` provides the energy release from
+reactions and can often be expressed in terms of the instantaneous
+reaction terms, :math:`\dot{X}_k`. As noted in the previous section,
+this is implemented in a network-specific manner.
 
 In this system, :math:`e` is equal to the total specific internal
 energy. This allows us to easily call the EOS during the burn to obtain the temperature.
@@ -223,7 +225,7 @@ flow is (for VODE):
    and zero out the temperature and energy derivatives if we are not integrating
    those quantities.
 
-#. apply any boosting if ``react_boost`` > 0
+#. apply any boosting if ``integrator.react_boost`` > 0
 
 
 Jacobian implementation
diff --git a/sphinx_docs/source/networks-overview.rst b/sphinx_docs/source/networks-overview.rst
index f4beb95e9..02074c1a7 100644
--- a/sphinx_docs/source/networks-overview.rst
+++ b/sphinx_docs/source/networks-overview.rst
@@ -114,9 +114,11 @@ There are two primary files within each network directory.
    state and (respectively) the time-derivatives and Jacobian
    elements to fill in.
 
-   Note: some networks do not provide an analytic Jacobian and instead
-   rely on the numerical difference-approximation to the Jacobian. In
-   this case, the interface ``actual_jac`` is still needed to compile.
+   .. note::
+
+      Some networks do not provide an analytic Jacobian and instead
+      rely on the numerical difference-approximation to the Jacobian. In
+      this case, the interface ``actual_jac`` is still needed to compile.
 
 Notice that these modules have initialization routines:
 
diff --git a/sphinx_docs/source/networks.rst b/sphinx_docs/source/networks.rst
index e0fd944f0..660054d3a 100644
--- a/sphinx_docs/source/networks.rst
+++ b/sphinx_docs/source/networks.rst
@@ -56,6 +56,8 @@ for plotfile variables, and the mass number, :math:`A`, and proton number, :math
 
 The name of the inputs file by one of two make variables:
 
+.. index:: NETWORK_INPUTS, GENERAL_NET_INPUTS
+
 * ``NETWORK_INPUTS`` : this is simply the name of the "`.net`" file, without
   any path.  The build system will look for it in the current directory
   and then in ``$(MICROPHYSICS_HOME)/networks/general_null/``.
diff --git a/sphinx_docs/source/nse.rst b/sphinx_docs/source/nse.rst
index 67b646b1f..98861252d 100644
--- a/sphinx_docs/source/nse.rst
+++ b/sphinx_docs/source/nse.rst
@@ -7,6 +7,8 @@ instead of integrating the entire network when the conditions are
 appropriate.  There are 2 different implementations of NSE in
 Microphysics, that have slightly different use cases.
 
+.. index:: USE_NSE_TABLE, USE_NSE_NET
+
 * :ref:`tabulated_nse` : this uses a table of NSE abundances given
   :math:`(\rho, T, Y_e)` generate from a large network (125 isotopes).
   The table also returns :math:`dY_e/dt` resulting from
diff --git a/sphinx_docs/source/one_zone_tests.rst b/sphinx_docs/source/one_zone_tests.rst
index ec9706a05..9352a2e62 100644
--- a/sphinx_docs/source/one_zone_tests.rst
+++ b/sphinx_docs/source/one_zone_tests.rst
@@ -9,6 +9,8 @@ on a single zone to inspect the output directly.
 ``burn_cell``
 =============
 
+.. index:: ``burn_cell``
+
 ``burn_cell`` is a simple one-zone burn that will evolve a state with
 a network for a specified amount of time.  This can be used to
 understand the timescales involved in a reaction sequence or to
diff --git a/sphinx_docs/source/preface.rst b/sphinx_docs/source/preface.rst
deleted file mode 100644
index efb680fb4..000000000
--- a/sphinx_docs/source/preface.rst
+++ /dev/null
@@ -1,30 +0,0 @@
-*******
-Preface
-*******
-
-Welcome to the AMReX-Astro Microphysics!
-
-In this User’s Guide we describe the microphysics modules designed to
-enable simulations of stellar explosions.
-
-The original design was to support the AMReX codes CASTRO and
-MAESTRO. These all have a consistent interface and are designed to
-provide the users of those codes an easy experience in moving from the
-barebones microphysics modules provided in those codes. For the
-purposes of this user’s guide, the microphysical components we
-currently deal with are the equation of state (EOS) and the nuclear
-burning network.
-
-Microphysics is not a stand-alone code. It is intended to be used in
-conjunction with a simulation code. At the moment, the interfaces and
-build stubs are compatible with the AMReX codes. In many cases we
-will provide test modules that demonstrate a minimal working example
-for how to run the modules (leveraging the AMReX build system). The
-goal is to make the support more general, and extend to other codes
-in the future.
-
-A number of the routines contained here we authored by other people.
-We bundle them here with permission, usually changing the interfaces
-to be compatible with our standardized interface. We in particular
-thank Frank Timmes for numerous reaction networks and his equation
-of state routines.
diff --git a/sphinx_docs/source/screening.rst b/sphinx_docs/source/screening.rst
index 1d99a925c..d1739aeb8 100644
--- a/sphinx_docs/source/screening.rst
+++ b/sphinx_docs/source/screening.rst
@@ -2,6 +2,8 @@
 Screening of Reaction Rates
 ***************************
 
+.. index:: SCREEN_METHOD
+
 Screening of reaction rates can be computed using several different methods,
 controlled by the make parameter ``SCREEN_METHOD``.  For example,
 
@@ -51,4 +53,12 @@ The options are:
 
 Runtime Options
 ----------------
-* ``screening.enable_chabrier1998_quantum_corr = 1`` in the input file enables an additional quantum correction term added to the screening factor when ``SCREEN_METHOD=chabrier1998``. This is disabled by default since ``chabrier1998`` is often used along with ``USE_NSE_NET=TRUE``, and the NSE solver doesn't include quantum corrections.
+
+.. index:: screening.enable_chabrier1998_quantum_corr
+
+* ``screening.enable_chabrier1998_quantum_corr = 1`` in the input file
+  enables an additional quantum correction term added to the screening
+  factor when ``SCREEN_METHOD=chabrier1998``. This is disabled by
+  default since ``chabrier1998`` is often used along with
+  ``USE_NSE_NET=TRUE``, and the NSE solver doesn't include quantum
+  corrections.
diff --git a/sphinx_docs/source/sdc.rst b/sphinx_docs/source/sdc.rst
index 3cbf8e7c3..38821a2a1 100644
--- a/sphinx_docs/source/sdc.rst
+++ b/sphinx_docs/source/sdc.rst
@@ -33,6 +33,7 @@ hydrodynamical sources),
 and :math:`\Rb(\Uc)`
 is the reaction source term.
 
+.. index:: USE_TRUE_SDC, USE_SIMPLIFIED_SDC
 
 .. note::
 
diff --git a/sphinx_docs/source/unit_tests.rst b/sphinx_docs/source/unit_tests.rst
index a95a18de7..5a36b2c4a 100644
--- a/sphinx_docs/source/unit_tests.rst
+++ b/sphinx_docs/source/unit_tests.rst
@@ -43,6 +43,8 @@ Tests are divided into three categories:
 Comprehensive tests
 ===================
 
+.. index:: test_aprox_rates, test_conductivity, test_eos, test_jac, test_neutrino_cooling, test_react, test_rhs, test_screening_templated, test_sdc
+
 Each of these tests sets up a cube of data, $(\rho, T, X_k)$, with the
 range of $T$ and $\rho$, and the species to focus on for $X_k$ controlled
 by options in the input file.
@@ -113,6 +115,8 @@ by options in the input file.
 One-zone tests
 ==============
 
+.. index:: burn_cell, burn_cell_primordial_chem, burn_cell_sdc, eos_cell, jac_cell, nse_table_cell, test_ase, test_part_func
+
 * ``burn_cell`` :
 
   given a $\rho$, $T$, and $X_k$, integrate a reaction network through a specified time
@@ -157,6 +161,8 @@ One-zone tests
 Infrastructure tests
 ====================
 
+.. index:: test_linear_algebra, test_nse_interp, test_parameters, test_sdc_vode_rhs
+
 * ``test_linear_algebra`` :
 
   create a diagonally dominant matrix, multiply it by a test vector, $x$,

From 48da3f8823d14f15db033c7ce4adf195122e9134 Mon Sep 17 00:00:00 2001
From: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon, 25 Nov 2024 11:46:33 -0500
Subject: [PATCH 12/13] fix some NSE documentation (#1670)

---
 sphinx_docs/source/nse.rst | 21 +++++----------------
 1 file changed, 5 insertions(+), 16 deletions(-)

diff --git a/sphinx_docs/source/nse.rst b/sphinx_docs/source/nse.rst
index 98861252d..f0dfb51cf 100644
--- a/sphinx_docs/source/nse.rst
+++ b/sphinx_docs/source/nse.rst
@@ -132,7 +132,7 @@ The basic flow of a simulation using ``aprox19`` + the NSE table is as follows:
     * use :math:`\rho`, :math:`T`, and :math:`Y_e` to call the table.
       This returns: :math:`dY_e/dt`, :math:`(B/A)_{\rm out}`, and :math:`\bar{A}_{\rm out}`.
 
-    * update :math:`Y_e` [#fY]_ :
+    * update :math:`Y_e` :
 
       .. math::
 
@@ -190,13 +190,13 @@ The composition check considers the following nuclei groups:
 
 and we then say that a composition supports NSE if:
 
-* :math:`X(C_group)` < ``C_nse``
+* :math:`X(C_\mathrm{group})` < ``C_nse``
 
-* :math:`X(O_group)` < ``O_nse``
+* :math:`X(O_\mathrm{group})` < ``O_nse``
 
-* :math:`X(Si_group)` < ``Si_nse``
+* :math:`X(Si_\mathrm{group})` < ``Si_nse``
 
-* :math:`X(Fe_group) + X(He_group)` > ``He_Fe_nse``
+* :math:`X(Fe_\mathrm{group}) + X(He_\mathrm{group})` > ``He_Fe_nse``
 
 
 
@@ -443,14 +443,3 @@ to the self-consistent nse check:
   the subsequent NSE checks. This is mainly to avoid unnecessary computations
   of computing the NSE mass fractions when the current temperature is too low.
   This is set to 4.0e9 by default.
-
-
-.. rubric:: Footnotes
-
-.. [#fY] The table actually provides the weak rate, which is the sum
-   of all electron capture and positron decay rates times the
-   appropriate abundances minus a similar rate for the beta decay and
-   positron capture, [wrate] = [rectot] + [rpdtot] - [redtot] - [rpctot]
-
-   So if electron capture dominates, then [wrate] is positive and this should
-   be subtracted from :math:`Y_e`.

From 161b785c01916e5a77ec0ef8817b57382ed1e95e Mon Sep 17 00:00:00 2001
From: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Sun, 1 Dec 2024 08:44:15 -0500
Subject: [PATCH 13/13] update changes for 24.12 (#1676)

---
 CHANGES.md | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/CHANGES.md b/CHANGES.md
index ab4a27674..224a10151 100644
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -1,10 +1,14 @@
-# 24.11
+# 24.12
 
-  * a new metal chemistry network was added (#1648, #1650, #1651)
+  * documentation improvements (#1661, #1667, #1670)
 
-  * add dust temperature to primordial chem (#1649)
+  * optimize tabular NSE EOS calls (#1668)
 
-  * documentation updates (#1652)
+  * CI fixes (#1666, #1671, #1675) and new partition function CI
+    (#1673)
+
+  * `burn_cell` can now initialize all mass fractions to be equal
+    (#1665)
 
 # 24.10