Merge branch 'doc_burn_cell_sdc' of github.com:zingale/Microphysics i…

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AMReX-Astro · Feb 14, 2025 · 9aff213 · 9aff213
2 parents 8feb066 + cf10ab0
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diff --git a/.github/workflows/dependencies/dependencies_hip.sh b/.github/workflows/dependencies/dependencies_hip.sh
@@ -33,7 +33,9 @@ sudo apt-key add rocm.gpg.key
 
 source /etc/os-release # set UBUNTU_CODENAME: focal or jammy or ...
 
-echo "deb [arch=amd64] https://repo.radeon.com/rocm/apt/${1-latest} ${UBUNTU_CODENAME} main" \
+VERSION=${1-6.3.2}
+
+echo "deb [arch=amd64] https://repo.radeon.com/rocm/apt/${VERSION} ${UBUNTU_CODENAME} main" \
   | sudo tee /etc/apt/sources.list.d/rocm.list
 echo 'export PATH=/opt/rocm/llvm/bin:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin:$PATH' \
   | sudo tee -a /etc/profile.d/rocm.sh
@@ -53,16 +55,16 @@ sudo apt-get install -y --no-install-recommends \
     libnuma-dev     \
     libopenmpi-dev  \
     openmpi-bin     \
-    rocm-dev        \
-    roctracer-dev   \
-    rocprofiler-dev \
-    rocrand-dev     \
-    rocfft-dev      \
-    rocprim-dev     \
-    rocsparse-dev
+    rocm-dev${VERSION}        \
+    roctracer-dev${VERSION}   \
+    rocprofiler-dev${VERSION} \
+    rocrand-dev${VERSION}     \
+    rocfft-dev${VERSION}      \
+    rocprim-dev${VERSION}     \
+    rocsparse-dev${VERSION}
 
 # hiprand-dev is a new package that does not exist in old versions
-sudo apt-get install -y --no-install-recommends hiprand-dev || true
+sudo apt-get install -y --no-install-recommends hiprand-dev${VERSION} || true
 
 # activate
 #

diff --git a/.github/workflows/hip.yml b/.github/workflows/hip.yml
@@ -8,7 +8,7 @@ concurrency:
 
 jobs:
   hip-compile:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
     steps:
       - uses: actions/checkout@v4
         with:
@@ -27,7 +27,7 @@ jobs:
           cd ../..
 
       - name: Dependencies
-        run: .github/workflows/dependencies/dependencies_hip.sh
+        run: .github/workflows/dependencies/dependencies_hip.sh 6.3.2
 
       - name: compile test_react with HIP (iso7)
         run: |

diff --git a/Docs/source/comprehensive_tests.rst b/Docs/source/comprehensive_tests.rst
@@ -1,3 +1,5 @@
+.. _sec:comprehensive_tests:
+
 ************************
 Comprehensive Unit Tests
 ************************

diff --git a/Docs/source/integrators.rst b/Docs/source/integrators.rst
@@ -88,7 +88,7 @@ routine (at the moment this can be ``VODE``, ``BackwardEuler``, ``ForwardEuler``
 .. code-block:: c++
 
     AMREX_GPU_HOST_DEVICE AMREX_FORCE_INLINE
-    void burner (burn_t& state, Real dt)
+    void burner (burn_t& state, amrex::Real dt)
 
 The input is a ``burn_t``.
 
@@ -198,7 +198,7 @@ be computed as:
 
 .. code-block:: c++
 
-      Array1D<Real, 1, NumSpec> y;
+      amrex::Array1D<amrex::Real, 1, NumSpec> y;
       ...
       for (int i = 1; i <= NumSpec; ++i) {
           y(i) = state.xn[i-1] * aion_inv[i-1];

diff --git a/Docs/source/one_zone_tests.rst b/Docs/source/one_zone_tests.rst
@@ -1,3 +1,5 @@
+.. _sec:one_zone_tests:
+
 **************
 One Zone Tests
 **************

diff --git a/Docs/source/templated_networks.rst b/Docs/source/templated_networks.rst
@@ -312,7 +312,7 @@ The main logic for constructing RHS is contained in ``Microphysics/networks/rhs.
 .. code:: c++
 
    AMREX_GPU_HOST_DEVICE AMREX_INLINE
-   void rhs (burn_t& state, Array1D<Real, 1, neqs>& ydot)
+   void rhs (burn_t& state, amrex::Array1D<amrex::Real, 1, neqs>& ydot)
 
 The basic flow is:
 

diff --git a/Docs/source/transport.rst b/Docs/source/transport.rst
@@ -85,7 +85,8 @@ 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,
+   void actual_opacity (amrex::Real& kp, amrex::Real& kr,
+                        amrex::Real rho, amrex::Real temp, amrex::Real rhoYe, amrex::Real nu,
                         bool get_Planck_mean, bool get_Rosseland_mean)
 
 where the boolean ``get_Planck_mean`` and ``get_Rosseland_mean`` specify where those

diff --git a/Docs/source/unit_test_runtime_parameters.rst b/Docs/source/unit_test_runtime_parameters.rst
@@ -25,7 +25,8 @@ Most of the unit tests require a composition to be defined (for the
 initial mass-fractions, $X_k$).  There are a few ways this can be done
 (depending on the test).
 
-* One-zone (``*_cell``) tests usually do one of:
+
+* One-zone (``*_cell``) tests (see :ref:`sec:one_zone_tests`) usually do one of:
 
   * *Explicitly setting the individual mass fractions.*  This is
     controlled by the parameters ``unit_test.X1``, ``unit_test.X2``, ..., ``unit_test.X35``,
@@ -45,7 +46,8 @@ initial mass-fractions, $X_k$).  There are a few ways this can be done
     ``unit_test.uniform_xn``.  If this is set to ``1``, then each mass fraction
     is initialized to ``1 / NumSpec``.
 
-* Comprehensive tests need many different compositions, since they are creating a cube
+* Comprehensive tests (see :ref:`sec:comprehensive_tests`) need many different compositions, since they are creating a cube
+
   of varying thermodynamic properties, and thus require a prescription
   to create the composition.  This is done by setting ``unit_test.primary_species_1``,
   ``unit_test.primary_species_2``, and ``unit_test.primary_species_3`` to one of the

diff --git a/EOS/multigamma/eos_composition.H b/EOS/multigamma/eos_composition.H
@@ -8,9 +8,9 @@
 using namespace amrex::literals;
 
 struct eos_xderivs_t {
-  Real dedX[NumSpec];
-  Real dpdX[NumSpec];
-  Real dhdX[NumSpec];
+  amrex::Real dedX[NumSpec];
+  amrex::Real dpdX[NumSpec];
+  amrex::Real dhdX[NumSpec];
 };
 
 // Given a set of mass fractions, calculate quantities that depend
@@ -32,7 +32,7 @@ void subroutine (T& state)
     }
     state.mu_e = 1.0_rt / state.y_e;
 
-    Real sum = 0.0_rt;
+    amrex::Real sum = 0.0_rt;
     for (int n = 0; n < NumSpec; ++n) {
         sum = sum + state.xn[n] * aion_inv[n];
     }
@@ -51,7 +51,7 @@ eos_x_derivs_t composition_derivatives (const T& state)
     eos_xderivs_t state_xderivs;
 
     // Get the mass of a nucleon from Avogadro's number.
-    const Real m_nucleon = 1.0_rt / n_A;
+    const amrex::Real m_nucleon = 1.0_rt / n_A;
 
     // Composition derivatives
 

diff --git a/EOS/ztwd/actual_eos.H b/EOS/ztwd/actual_eos.H
@@ -27,9 +27,9 @@ using namespace amrex::literals;
 
 const std::string eos_name = "ztwd";
 
-const Real A = M_PI * amrex::Math::powi<4>(C::m_e) * amrex::Math::powi<5>(C::c_light) / (3.0_rt * amrex::Math::powi<3>(C::hplanck));
-const Real B2 = 8.0_rt * M_PI * amrex::Math::powi<3>(C::m_e) * amrex::Math::powi<3>(C::c_light) * C::m_p  / (3.0_rt * amrex::Math::powi<3>(C::hplanck));
-const Real iter_tol = 1.e-10_rt;
+const amrex::Real A = M_PI * amrex::Math::powi<4>(C::m_e) * amrex::Math::powi<5>(C::c_light) / (3.0_rt * amrex::Math::powi<3>(C::hplanck));
+const amrex::Real B2 = 8.0_rt * M_PI * amrex::Math::powi<3>(C::m_e) * amrex::Math::powi<3>(C::c_light) * C::m_p  / (3.0_rt * amrex::Math::powi<3>(C::hplanck));
+const amrex::Real iter_tol = 1.e-10_rt;
 const int  max_iter = 1000;
 
 inline
@@ -43,7 +43,7 @@ AMREX_GPU_HOST_DEVICE AMREX_INLINE
 bool is_input_valid (I input)
 {
   static_assert(std::is_same_v<I, eos_input_t>, "input must be an eos_input_t");
-
+  amrex::ignore_unused(input);
   bool valid = true;
 
   return valid;
@@ -52,23 +52,23 @@ bool is_input_valid (I input)
 
 
 AMREX_GPU_HOST_DEVICE AMREX_INLINE
-Real pressure (Real x)
+amrex::Real pressure (amrex::Real x)
 {
     return A * (x * (2.0_rt * x * x - 3.0_rt) * std::sqrt(x * x + 1.0_rt) + 3.0_rt * std::asinh(x));
 }
 
 
 
 AMREX_GPU_HOST_DEVICE AMREX_INLINE
-Real enthalpy (Real x, Real B)
+amrex::Real enthalpy (amrex::Real x, amrex::Real B)
 {
     return (8.0_rt * A / B) * std::sqrt(1.0_rt + x * x);
 }
 
 
 
 AMREX_GPU_HOST_DEVICE AMREX_INLINE
-Real dpdx (Real x)
+amrex::Real dpdx (amrex::Real x)
 {
     return A * ((2.0_rt * x * x - 3.0_rt) * std::sqrt(x * x + 1.0_rt) +
                 x * (4.0_rt * x) * std::sqrt(x * x + 1.0_rt) +
@@ -79,7 +79,7 @@ Real dpdx (Real x)
 
 
 AMREX_GPU_HOST_DEVICE AMREX_INLINE
-Real dhdx (Real x, Real B)
+amrex::Real dhdx (amrex::Real x, amrex::Real B)
 {
     return enthalpy(x, B) * (x / (x * x + 1.0_rt));
 }
@@ -88,12 +88,12 @@ Real dhdx (Real x, Real B)
 
 
 AMREX_GPU_HOST_DEVICE AMREX_INLINE
-void pres_iter (Real pres, Real& dens, Real B)
+void pres_iter (amrex::Real pres, amrex::Real& dens, amrex::Real B)
 {
 
     // Starting guess for the iteration.
 
-    Real x = 1.0_rt;
+    amrex::Real x = 1.0_rt;
 
     // We are solving the equation:
     // f(x) = p_want - p(x) = 0.
@@ -104,7 +104,7 @@ void pres_iter (Real pres, Real& dens, Real B)
 
     for (iter = 1; iter <= max_iter; ++iter)
     {
-        Real dx = (pres - pressure(x)) / dpdx(x);
+        amrex::Real dx = (pres - pressure(x)) / dpdx(x);
 
         x = x + dx;
 
@@ -131,32 +131,32 @@ void actual_eos (I input, T& state)
 {
     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;
+    amrex::Real dens = state.rho;
+    amrex::Real temp = state.T;
 
-    Real pres = 1.0_rt;
+    amrex::Real pres = 1.0_rt;
     if constexpr (has_pressure<T>::value) {
         pres = state.p;
     }
 
-    Real enth = 1.0_rt;
+    amrex::Real enth = 1.0_rt;
     if constexpr (has_enthalpy<T>::value) {
         enth = state.h;
     }
 
-    Real eint = 1.0_rt;
+    amrex::Real eint = 1.0_rt;
     if constexpr (has_energy<T>::value) {
         eint = state.e;
     }
 
-    Real entr = 1.0_rt;
+    amrex::Real entr = 1.0_rt;
     if constexpr (has_entropy<T>::value) {
         entr = state.s;
     }
 
-    Real B = B2 * state.mu_e;
+    amrex::Real B = B2 * state.mu_e;
 
-    Real x, dxdr;
+    amrex::Real x, dxdr;
 
     switch (input) {
 
@@ -321,8 +321,8 @@ void actual_eos (I input, T& state)
     x = std::cbrt(dens / B);
     dxdr = (1.0_rt / 3.0_rt) * x / dens;
 
-    Real dpdr = dxdr * dpdx(x);
-    Real dhdr = dxdr * dhdx(x, B);
+    amrex::Real dpdr = dxdr * dpdx(x);
+    amrex::Real dhdr = dxdr * dhdx(x, B);
 
     if constexpr (has_pressure<T>::value) {
         state.dpdr = dpdr;

diff --git a/conductivity/stellar/actual_conductivity.H b/conductivity/stellar/actual_conductivity.H
@@ -127,9 +127,7 @@ actual_conductivity (T& state)
    amrex::Real xkaz = 50.0_rt*xz*xka1 * std::exp(-0.5206_rt*amrex::Math::powi<2>((std::log(state.rho)-d0log)/xkw));
    amrex::Real dbar2log = -(4.283_rt + 0.7196_rt*xh) + 3.86_rt*std::log(t6);
    amrex::Real dbar1log = -5.296_rt + 4.833_rt*std::log(t6);
-   if (dbar2log < dbar1log) {
-     dbar1log = dbar2log;
-   }
+   dbar1log = std::min(dbar1log, dbar2log);
    oiben2 = std::pow(state.rho/std::exp(dbar1log), 0.67_rt) * std::exp(xkaz);
   }
 

diff --git a/integration/nse_update_sdc.H b/integration/nse_update_sdc.H
@@ -1,8 +1,6 @@
 #ifndef NSE_UPDATE_H
 #define NSE_UPDATE_H
 
-#include <AMReX_Algorithm.H>
-
 #include <iostream>
 #include <fstream>
 #include <actual_network.H>

diff --git a/integration/utils/nonaka_plot.H b/integration/utils/nonaka_plot.H
@@ -52,7 +52,7 @@ void nonaka_init() {
 
 template <typename BurnT>
 AMREX_GPU_HOST_DEVICE AMREX_FORCE_INLINE
-void nonaka_rhs(const Real time, const BurnT& state, const YdotNetArray1D& ydot_react) {
+void nonaka_rhs(const amrex::Real time, const BurnT& state, const YdotNetArray1D& ydot_react) {
 
     // state: the burn_t corresponding to the current state note:
     // state.time is relative to the start of the current burn call,
@@ -74,7 +74,7 @@ void nonaka_rhs(const Real time, const BurnT& state, const YdotNetArray1D& ydot_
         nf.open(nonaka_file, std::ios::app);
 
 
-        Real simulation_time = time + state.reference_time;
+        amrex::Real simulation_time = time + state.reference_time;
 
         nf << std::setw(FIELD_WIDTH) << simulation_time << " ";
 

diff --git a/networks/aprox21/actual_network.H b/networks/aprox21/actual_network.H
@@ -235,7 +235,7 @@ namespace RHS {
 
         rhs_t data;
 
-        switch (rate) {
+        switch (rate) {  // NOLINT(bugprone-switch-missing-default-case)
 
         case P_to_N:
             // irpen and irnep in the original aprox21

diff --git a/nse_solver/nse_eos.H b/nse_solver/nse_eos.H
@@ -102,7 +102,7 @@ nse_T_abar_from_e(const amrex::Real rho, const amrex::Real e_in,
                   amrex::Real &T, amrex::Real &abar,
                   amrex::Real &mu_p, amrex::Real &mu_n) {
 
-    constexpr Real ttol{1.e-8_rt};
+    constexpr amrex::Real ttol{1.e-8_rt};
     constexpr int max_iter{100};
 
     bool converged{false};
@@ -148,8 +148,8 @@ nse_T_abar_from_e(const amrex::Real rho, const amrex::Real e_in,
 
         // compute the correction to our guess
 
-        Real dT = -f / (eos_state.dedT + eos_state.dedA * dabar_dT
-                                  + Ye * eos_state.dedZ * dabar_dT);
+        amrex::Real dT = -f / (eos_state.dedT + eos_state.dedA * dabar_dT
+                               + Ye * eos_state.dedZ * dabar_dT);
 
         // update the temperature and abar
 

diff --git a/opacity/breakout/actual_opacity.H b/opacity/breakout/actual_opacity.H
@@ -9,11 +9,12 @@ AMREX_INLINE
 void actual_opacity_init () {}
 
 AMREX_GPU_HOST_DEVICE AMREX_INLINE
-void actual_opacity (Real& kp, Real& kr, Real rho, Real temp, Real rhoYe, Real nu,
+void actual_opacity (amrex::Real& kp, amrex::Real& kr,
+                     amrex::Real rho, amrex::Real temp, amrex::Real rhoYe, amrex::Real nu,
                      bool get_Planck_mean, bool get_Rosseland_mean)
 {
-    const Real Ksc = 0.4e0; // Thomson scattering
-    const Real fac = 1.e-4; // Planck mean is assumed to be fac * Ksc
+    const amrex::Real Ksc = 0.4e0; // Thomson scattering
+    const amrex::Real fac = 1.e-4; // Planck mean is assumed to be fac * Ksc
 
     if (get_Planck_mean) {
         kp = rhoYe * Ksc * fac;
@@ -25,5 +26,3 @@ void actual_opacity (Real& kp, Real& kr, Real rho, Real temp, Real rhoYe, Real n
 }
 
 #endif
-
-
diff --git a/opacity/opacity.H b/opacity/opacity.H
@@ -10,7 +10,8 @@ void opacity_init ()
 }
 
 AMREX_GPU_HOST_DEVICE AMREX_INLINE
-void opacity (Real& kp, Real& kr, Real rho, Real temp, Real rhoYe, Real nu,
+void opacity (Real& kp, amrex::Real& kr, amrex::Real rho,
+              amrex::Real temp, amrex::Real rhoYe, amrex::Real nu,
               bool get_Planck_mean, bool get_Rosseland_mean)
 {
     actual_opacity(kp, kr, rho, temp, rhoYe, nu, get_Planck_mean, get_Rosseland_mean);