Merge branch 'development' into ROCK4

.clang-tidy

@@ -6,7 +6,6 @@ Checks: >
      clang-diagnostic-*,
      cppcoreguidelines-*,
        -cppcoreguidelines-avoid-c-arrays,
-       -cppcoreguidelines-avoid-goto,
        -cppcoreguidelines-avoid-magic-numbers,
        -cppcoreguidelines-avoid-non-const-global-variables,
        -cppcoreguidelines-init-variables,
@@ -16,11 +15,19 @@ Checks: >
        -cppcoreguidelines-non-private-member-variables-in-classes,
        -cppcoreguidelines-owning-memory,
        -cppcoreguidelines-pro-*,
+     misc-*,
+       -misc-const-correctness,
+       -misc-include-cleaner,
+       -misc-non-private-member-variables-in-classes,
+       -misc-no-recursion,
+       -misc-use-anonymous-namespace,
      modernize-*,
        -modernize-avoid-c-arrays,
        -modernize-use-trailing-return-type,
        -modernize-use-using,
      performance-*,
+       -performance-avoid-endl,
+     portability-*,
      readability-*,
        -readability-avoid-const-params-in-decls,
        -readability-braces-around-statements,

.github/dependabot.yml

@@ -0,0 +1,16 @@
+# Dependabot configuration
+# ref: https://docs.github.com/en/code-security/supply-chain-security/keeping-your-dependencies-updated-automatically/configuration-options-for-dependency-updates
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    target-branch: "development"
+
+  - package-ecosystem: "pip"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    target-branch: "development"
+

.github/workflows/castro-development.yml

@@ -29,7 +29,7 @@ jobs:
         .github/workflows/dependencies/dependencies.sh
         .github/workflows/dependencies/dependencies_ccache.sh
     - name: Set Up Cache
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: ~/.cache/ccache
         key: ccache-${{ github.workflow }}-${{ github.job }}-git-${{ github.sha }}
@@ -78,7 +78,7 @@ jobs:
           PR_NUMBER: ${{ github.event.number }}
         run: |
           echo $PR_NUMBER > pr_number.txt
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           name: pr_number
           path: pr_number.txt

.github/workflows/castro.yml

@@ -33,7 +33,7 @@ jobs:
         .github/workflows/dependencies/dependencies.sh
         .github/workflows/dependencies/dependencies_ccache.sh
     - name: Set Up Cache
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: ~/.cache/ccache
         key: ccache-${{ github.workflow }}-${{ github.job }}-git-${{ github.sha }}
@@ -82,7 +82,7 @@ jobs:
           PR_NUMBER: ${{ github.event.number }}
         run: |
           echo $PR_NUMBER > pr_number.txt
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           name: pr_number
           path: pr_number.txt

.github/workflows/check_powi.yml

@@ -14,17 +14,17 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
       - name: Setup Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: '3.10'
 
       - name: Cache pip
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           # this path is specific to Ubuntu
           path: ~/.cache/pip

CHANGES.md

@@ -1,3 +1,21 @@
+# 24.02
+
+   * Lots of general code cleaning from coverity and clang-tidy
+     (#1450, #1452, #1453, #1460, #1459, #1457, #1458)
+
+   * Fixed a bug in the VODE pivoting when a cached Jacobian is used
+     (#1456)
+
+   * Added reverse rates to CNO_extras (#1445)
+
+   * Sync networks up with pynucastro to get constexpr mion/bion
+     (#1437)
+
+   * NSE+SDC improvements (#1431)
+
+   * Start of moving the runtime parameters from globals to structs
+     (#1422)
+
 # 24.01
 
    * The quantum corrections for the Chabrier screening are

EOS/breakout/actual_eos.H

@@ -29,7 +29,7 @@ template <typename I>
 AMREX_GPU_HOST_DEVICE AMREX_INLINE
 bool is_input_valid (I input)
 {
-  static_assert(std::is_same<I, eos_input_t>::value, "input must be an eos_input_t");
+  static_assert(std::is_same_v<I, eos_input_t>, "input must be an eos_input_t");
 
   bool valid = true;
 
@@ -48,7 +48,7 @@ template <typename I, typename T>
 AMREX_GPU_HOST_DEVICE AMREX_INLINE
 void actual_eos (I input, T& state)
 {
-    static_assert(std::is_same<I, eos_input_t>::value, "input must be an eos_input_t");
+    static_assert(std::is_same_v<I, eos_input_t>, "input must be an eos_input_t");
 
     const Real R = C::k_B * C::n_A;
 

EOS/gamma_law/actual_eos.H

@@ -34,7 +34,7 @@ template <typename I>
 AMREX_GPU_HOST_DEVICE AMREX_INLINE
 bool is_input_valid (I input)
 {
-  static_assert(std::is_same<I, eos_input_t>::value, "input must be an eos_input_t");
+  static_assert(std::is_same_v<I, eos_input_t>, "input must be an eos_input_t");
 
   bool valid = true;
 
@@ -50,7 +50,7 @@ template <typename I, typename T>
 AMREX_GPU_HOST_DEVICE AMREX_INLINE
 void actual_eos (I input, T& state)
 {
-    static_assert(std::is_same<I, eos_input_t>::value, "input must be an eos_input_t");
+    static_assert(std::is_same_v<I, eos_input_t>, "input must be an eos_input_t");
 
     // Get the mass of a nucleon from m_u.
     const Real m_nucleon = C::m_u;

EOS/helmholtz/actual_eos.H

@@ -1238,7 +1238,7 @@ template <typename I, typename T>
 AMREX_GPU_HOST_DEVICE AMREX_INLINE
 void actual_eos (I input, T& state)
 {
-    static_assert(std::is_same<I, eos_input_t>::value, "input must be an eos_input_t");
+    static_assert(std::is_same_v<I, eos_input_t>, "input must be an eos_input_t");
 
     using namespace helmholtz;
 
@@ -1489,7 +1489,7 @@ bool is_input_valid (I input)
 {
   amrex::ignore_unused(input);
 
-  static_assert(std::is_same<I, eos_input_t>::value, "input must be an eos_input_t");
+  static_assert(std::is_same_v<I, eos_input_t>, "input must be an eos_input_t");
 
   bool valid = true;
 

EOS/multigamma/actual_eos.H

@@ -53,7 +53,7 @@ template <typename I>
 AMREX_GPU_HOST_DEVICE AMREX_INLINE
 bool is_input_valid (I input)
 {
-  static_assert(std::is_same<I, eos_input_t>::value, "input must be an eos_input_t");
+  static_assert(std::is_same_v<I, eos_input_t>, "input must be an eos_input_t");
 
   bool valid = true;
 
@@ -70,7 +70,7 @@ template <typename I, typename T>
 AMREX_GPU_HOST_DEVICE AMREX_INLINE
 void actual_eos (I input, T& state)
 {
-    static_assert(std::is_same<I, eos_input_t>::value, "input must be an eos_input_t");
+    static_assert(std::is_same_v<I, eos_input_t>, "input must be an eos_input_t");
 
     // Get the mass of a nucleon from Avogadro's number.
     const Real m_nucleon = 1.0_rt / C::n_A;

EOS/polytrope/actual_eos.H

@@ -79,7 +79,7 @@ template <typename I>
 AMREX_GPU_HOST_DEVICE AMREX_INLINE
 bool is_input_valid (I input)
 {
-  static_assert(std::is_same<I, eos_input_t>::value, "input must be an eos_input_t");
+  static_assert(std::is_same_v<I, eos_input_t>, "input must be an eos_input_t");
 
   bool valid = true;
 
@@ -122,7 +122,7 @@ template <typename I, typename T>
 AMREX_GPU_HOST_DEVICE AMREX_INLINE
 void actual_eos (I input, T& state)
 {
-    static_assert(std::is_same<I, eos_input_t>::value, "input must be an eos_input_t");
+    static_assert(std::is_same_v<I, eos_input_t>, "input must be an eos_input_t");
 
     Real dens = state.rho;
     Real temp = state.T;

EOS/primordial_chem/actual_eos.H

@@ -120,7 +120,7 @@ template <typename I>
 AMREX_GPU_HOST_DEVICE AMREX_INLINE
 bool is_input_valid (I input)
 {
-  static_assert(std::is_same<I, eos_input_t>::value, "input must be either eos_input_rt or eos_input_re");
+  static_assert(std::is_same_v<I, eos_input_t>, "input must be either eos_input_rt or eos_input_re");
 
   bool valid = false;
 
@@ -137,7 +137,7 @@ template <typename I, typename T>
 AMREX_GPU_HOST_DEVICE AMREX_INLINE
 void actual_eos (I input, T& state)
 {
-    static_assert(std::is_same<I, eos_input_t>::value, "input must be either eos_input_rt or eos_input_re");
+    static_assert(std::is_same_v<I, eos_input_t>, "input must be either eos_input_rt or eos_input_re");
 
     const Real gasconstant = C::n_A * C::k_B;
     const Real protonmass = C::m_p;

EOS/rad_power_law/actual_eos.H

@@ -49,7 +49,7 @@ template <typename I>
 AMREX_GPU_HOST_DEVICE AMREX_INLINE
 bool is_input_valid (I input)
 {
-  static_assert(std::is_same<I, eos_input_t>::value, "input must be an eos_input_t");
+  static_assert(std::is_same_v<I, eos_input_t>, "input must be an eos_input_t");
 
   bool valid = true;
 
@@ -70,7 +70,7 @@ template <typename I, typename T>
 AMREX_GPU_HOST_DEVICE AMREX_INLINE
 void actual_eos (I input, T& state)
 {
-    static_assert(std::is_same<I, eos_input_t>::value, "input must be an eos_input_t");
+    static_assert(std::is_same_v<I, eos_input_t>, "input must be an eos_input_t");
 
     switch (input) {
 

EOS/tillotson/actual_eos.H

@@ -27,7 +27,7 @@ template <typename I>
 AMREX_GPU_HOST_DEVICE AMREX_INLINE
 bool is_input_valid (I input)
 {
-  static_assert(std::is_same<I, eos_input_t>::value, "input must be an eos_input_t");
+  static_assert(std::is_same_v<I, eos_input_t>, "input must be an eos_input_t");
 
   bool valid = false;
 
@@ -47,7 +47,7 @@ template <typename I, typename T>
 AMREX_GPU_HOST_DEVICE AMREX_INLINE
 void actual_eos (I input, T& state)
 {
-    static_assert(std::is_same<I, eos_input_t>::value, "input must be an eos_input_t");
+    static_assert(std::is_same_v<I, eos_input_t>, "input must be an eos_input_t");
 
     // First make T and e consistent with each other.
     // We assume a simple relationship between energy and temperature.

EOS/ztwd/actual_eos.H

@@ -42,7 +42,7 @@ template <typename I>
 AMREX_GPU_HOST_DEVICE AMREX_INLINE
 bool is_input_valid (I input)
 {
-  static_assert(std::is_same<I, eos_input_t>::value, "input must be an eos_input_t");
+  static_assert(std::is_same_v<I, eos_input_t>, "input must be an eos_input_t");
 
   bool valid = true;
 
@@ -129,7 +129,7 @@ template <typename I, typename T>
 AMREX_GPU_HOST_DEVICE AMREX_INLINE
 void actual_eos (I input, T& state)
 {
-    static_assert(std::is_same<I, eos_input_t>::value, "input must be an eos_input_t");
+    static_assert(std::is_same_v<I, eos_input_t>, "input must be an eos_input_t");
 
     Real dens = state.rho;
     Real temp = state.T;

integration/VODE/actual_integrator.H

@@ -79,9 +79,9 @@ void actual_integrator (BurnT& state, Real dt)
     for (int n = 0; n < NumSpec; ++n) {
         xn_in[n] = state.xn[n];
     }
-    Real T_in = state.T;
+    const Real T_in = state.T;
 #endif
-    Real e_in = state.e;
+    const Real e_in = state.e;
 
     // Call the integration routine.
 
@@ -173,14 +173,14 @@ void actual_integrator (BurnT& state, Real dt)
             std::cout << "dt = " << std::setprecision(16) << dt << std::endl;
             std::cout << "temp start = " << std::setprecision(16) << T_in << std::endl;
             std::cout << "xn start = ";
-            for (double x : xn_in) {
+            for (const double x : xn_in) {
                 std::cout << std::setprecision(16) << x << " ";
             }
             std::cout << std::endl;
             std::cout << "dens current = " << std::setprecision(16) << state.rho << std::endl;
             std::cout << "temp current = " << std::setprecision(16) << state.T << std::endl;
             std::cout << "xn current = ";
-            for (double x : state.xn) {
+            for (const double x : state.xn) {
                 std::cout << std::setprecision(16) << x << " ";
             }
             std::cout << std::endl;

integration/VODE/vode_dvhin.H

@@ -26,8 +26,8 @@ void dvhin (BurnT& state, DvodeT& vstate, Real& H0, int& NITER, int& IER)
     const Real PT1 = 0.1e0_rt;
 
     NITER = 0;
-    Real TDIST = std::abs(vstate.tout - vstate.t);
-    Real TROUND = UROUND * amrex::max(std::abs(vstate.t), std::abs(vstate.tout));
+    const Real TDIST = std::abs(vstate.tout - vstate.t);
+    const Real TROUND = UROUND * amrex::max(std::abs(vstate.t), std::abs(vstate.tout));
 
     if (TDIST < 2.0_rt * TROUND) {
         // Error return for vstate.tout - vstate.t too small.
@@ -36,15 +36,15 @@ void dvhin (BurnT& state, DvodeT& vstate, Real& H0, int& NITER, int& IER)
     }
 
     // Set a lower bound on h based on the roundoff level in vstate.t and vstate.tout.
-    Real HLB = 100.0_rt * TROUND;
+    const Real HLB = 100.0_rt * TROUND;
 
     // Set an upper bound on h based on vstate.tout-vstate.t and the initial Y and YDOT.
     Real HUB = PT1 * TDIST;
 
     for (int i = 1; i <= int_neqs; ++i) {
-        Real atol = i <= NumSpec ? vstate.atol_spec : vstate.atol_enuc;
-        Real DELYI = PT1 * std::abs(vstate.yh(i,1)) + atol;
-        Real AFI = std::abs(vstate.yh(i,2));
+        const Real atol = i <= NumSpec ? vstate.atol_spec : vstate.atol_enuc;
+        const Real DELYI = PT1 * std::abs(vstate.yh(i,1)) + atol;
+        const Real AFI = std::abs(vstate.yh(i,2));
         if (AFI * HUB > DELYI) {
             HUB = DELYI / AFI;
         }
@@ -61,14 +61,14 @@ void dvhin (BurnT& state, DvodeT& vstate, Real& H0, int& NITER, int& IER)
         do_iterations = false;
     }
 
-    Real hnew;
+    Real hnew{};
 
     if (do_iterations) {
 
         while (true) {
 
             // Estimate the second derivative as a difference quotient in f.
-            Real H = std::copysign(HG, vstate.tout - vstate.t);
+            const Real H = std::copysign(HG, vstate.tout - vstate.t);
             for (int i = 1; i <= int_neqs; ++i) {
                 vstate.y(i) = vstate.yh(i,1) + H * vstate.yh(i,2);
             }
@@ -106,7 +106,7 @@ void dvhin (BurnT& state, DvodeT& vstate, Real& H0, int& NITER, int& IER)
                 break;
             }
 
-            Real HRAT = hnew / HG;
+            const Real HRAT = hnew / HG;
             if ((HRAT > 0.5_rt) && (HRAT < 2.0_rt)) {
                 break;
             }