Merge branch 'development' into joss_paper

.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-*,

.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: |

.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

.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

.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

.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

.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
 

.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

.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

.github/workflows/macos_build_cell_metal_chem.yml

@@ -12,11 +12,10 @@ jobs:
       - name: Install dependencies
         run: |
           brew install cmake openmpi python3 || true
-          brew link --overwrite python@3.11
 
       - name: Compile and run
         run: |
           mkdir build && cd build
           cmake .. -DBUILD_UNIT_TEST_MC=true -DBUILD_AMReX=true
-          make -j2
+          make -j 4
           ctest --output-on-failure

.github/workflows/macos_build_cell_primordial_chem.yml

@@ -12,11 +12,10 @@ jobs:
       - name: Install dependencies
         run: |
           brew install cmake openmpi python3 || true
-          brew link --overwrite python@3.11
 
       - name: Compile and run
         run: |
           mkdir build && cd build
           cmake .. -DBUILD_UNIT_TEST_PC=true -DBUILD_AMReX=true
-          make -j2
+          make -j 4
           ctest --output-on-failure

.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: |

.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
+

.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: |

CHANGES.md

@@ -1,3 +1,15 @@
+# 24.12
+
+  * documentation improvements (#1661, #1667, #1670)
+
+  * optimize tabular NSE EOS calls (#1668)
+
+  * 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
 
   * metal chemistry updates (#1648) with ices (#1650) and cosmic rays (#1651)

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;

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,

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,

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,

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,

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)}")
 

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)}")
 

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;

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

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
@@ -89,14 +93,18 @@ 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.
 
 ``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: