Merge branch 'development' into gift_testing

AMReX-Astro · Aug 1, 2024 · 4db8a56 · 4db8a56
2 parents 1140337 + 14b8b0e
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diff --git a/.github/workflows/cuda.yml b/.github/workflows/cuda.yml
@@ -41,8 +41,8 @@ jobs:
           make realclean
           make NETWORK_DIR=ignition_reaclib/URCA-simple USE_CUDA=TRUE COMP=gnu USE_MPI=FALSE -j 2
 
-      - name: compile test_ase (ase)
+      - name: compile test_nse_net (ase)
         run: |
           export PATH=/usr/local/nvidia/bin:/usr/local/cuda/bin:${PATH}
-          cd unit_test/test_ase
+          cd unit_test/test_nse_net
           make USE_CUDA=TRUE COMP=gnu USE_MPI=FALSE -j 2
diff --git a/.github/workflows/good_defines.txt b/.github/workflows/good_defines.txt
@@ -1,3 +1,4 @@
+ALLOW_GPU_PRINTF
 ALLOW_JACOBIAN_CACHING
 AMREX_USE_CUDA
 AMREX_USE_GPU

diff --git a/.github/workflows/nse_test.yml → .github/workflows/jac_cell.yml b/.github/workflows/nse_test.yml → .github/workflows/jac_cell.yml
@@ -1,8 +1,8 @@
-name: nse_test
+name: jac_cell
 
 on: [pull_request]
 jobs:
-  nse_test:
+  nse_table:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
@@ -26,23 +26,20 @@ jobs:
           sudo apt-get update -y -qq
           sudo apt-get -qq -y install curl cmake jq clang g++>=9.3.0
 
-      - name: Compile, test_nse (aprox21)
+      - name: Compile jac_cell
         run: |
-          cd unit_test/test_nse
-          make realclean
-          make NETWORK_DIR=aprox21 -j 4
+          cd unit_test/jac_cell
+          make -j 4
 
-      - name: Run test_nse (aprox21)
+      - name: Run jac_cell
         run: |
-          cd unit_test/test_nse
-          ./main3d.gnu.ex inputs_aprox21 amrex.fpe_trap_{invalid,zero,overflow}=1 > test.out
+          cd unit_test/jac_cell
+          ./main3d.gnu.ex inputs_aprox13 > test.out
 
-      - name: Print backtrace
-        if: ${{ failure() && hashFiles('unit_test/test_nse/Backtrace.0') != '' }}
-        run: cat unit_test/test_nse/Backtrace.0
-
-      - name: Compare to stored output (aprox21)
+      - name: Compare to stored output
         run: |
-          cd unit_test/test_nse
-          diff -I "^Initializing AMReX" -I "^AMReX" -I "^reading in reaclib rates" -I "^0x" test.out ci-benchmarks/aprox21_ci.out
+          cd unit_test/jac_cell
+          diff -I "^Initializing AMReX" -I "^AMReX"  test.out ci-benchmarks/jac_cell_aprox13.out
+
+
 
diff --git a/.github/workflows/nse_net.yml b/.github/workflows/nse_net.yml
@@ -26,42 +26,42 @@ jobs:
           sudo apt-get update -y -qq
           sudo apt-get -qq -y install curl cmake jq clang g++>=9.3.0
 
-      - name: Compile, test_ase (NSE_NET, ase)
+      - name: Compile, test_nse_net (NSE_NET, ase)
         run: |
-          cd unit_test/test_ase
+          cd unit_test/test_nse_net
           make realclean
           make -j 4
 
-      - name: Run test_ase (NSE_NET, ase)
+      - name: Run test_nse_net (NSE_NET, ase)
         run: |
-          cd unit_test/test_ase
+          cd unit_test/test_nse_net
           ./main3d.gnu.ex inputs_ase amrex.fpe_trap_{invalid,zero,overflow}=1 > test.out
 
       - name: Print backtrace
-        if: ${{ failure() && hashFiles('unit_test/test_ase/Backtrace.0') != '' }}
-        run: cat unit_test/test_ase/Backtrace.0
+        if: ${{ failure() && hashFiles('unit_test/test_nse_net/Backtrace.0') != '' }}
+        run: cat unit_test/test_nse_net/Backtrace.0
 
       - name: Compare to stored output (NSE_NET, ase)
         run: |
-          cd unit_test/test_ase
-          diff -I "^Initializing AMReX" -I "^AMReX" -I "^reading in reaclib rates" test.out ci-benchmarks/ase_nse_net_unit_test.out
+          cd unit_test/test_nse_net
+          diff -I "^Initializing AMReX" -I "^AMReX" -I "^reading in reaclib rates" test.out ci-benchmarks/nse_net_unit_test.out
 
-      - name: Compile, test_ase/make_table (NSE_NET, ase, make_table)
+      - name: Compile, test_nse_net/make_table (NSE_NET, ase, make_table)
         run: |
-          cd unit_test/test_ase/make_table
+          cd unit_test/test_nse_net/make_table
           make realclean
           make -j 4
 
-      - name: Run, test_ase/make_table (NSE_NET, ase, make_table)
+      - name: Run, test_nse_net/make_table (NSE_NET, ase, make_table)
         run: |
-          cd unit_test/test_ase/make_table
+          cd unit_test/test_nse_net/make_table
           ./main3d.gnu.ex amrex.fpe_trap_{invalid,zero,overflow}=1 > test.out
 
       - name: Print backtrace
-        if: ${{ failure() && hashFiles('unit_test/test_ase/make_table/Backtrace.0') != '' }}
-        run: cat unit_test/test_ase/make_table/Backtrace.0
+        if: ${{ failure() && hashFiles('unit_test/test_nse_net/make_table/Backtrace.0') != '' }}
+        run: cat unit_test/test_nse_net/make_table/Backtrace.0
 
       - name: Compare to stored output (NSE_NET, ase, make_table)
         run: |
-          cd unit_test/test_ase/make_table
-          diff -I "^Initializing AMReX" -I "^AMReX" -I "^reading in reaclib rates" test.out ci-benchmarks/ase_nse_net_make_table_unit_test.out
+          cd unit_test/test_nse_net/make_table
+          diff -I "^Initializing AMReX" -I "^AMReX" -I "^reading in reaclib rates" test.out ci-benchmarks/nse_net_make_table_unit_test.out
diff --git a/.github/workflows/nse_table.yml b/.github/workflows/nse_table.yml
@@ -26,26 +26,6 @@ jobs:
           sudo apt-get update -y -qq
           sudo apt-get -qq -y install curl cmake jq clang g++>=9.3.0
 
-      - name: Compile, burn_cell (NSE, aprox19)
-        run: |
-          cd unit_test/burn_cell
-          make realclean
-          make NETWORK_DIR=aprox19 USE_NSE_TABLE=TRUE INTEGRATOR_DIR=VODE -j 4
-
-      - name: Run burn_cell (NSE, aprox19)
-        run: |
-          cd unit_test/burn_cell
-          ./main3d.gnu.ex inputs_aprox19.nse amrex.fpe_trap_{invalid,zero,overflow}=1 > test.out
-
-      - name: Print backtrace
-        if: ${{ failure() && hashFiles('unit_test/burn_cell/Backtrace.0') != '' }}
-        run: cat unit_test/burn_cell/Backtrace.0
-
-      - name: Compare to stored output (NSE, aprox19)
-        run: |
-          cd unit_test/burn_cell
-          diff -I "^Initializing AMReX" -I "^AMReX" -I "^reading in reaclib rates" test.out ci-benchmarks/aprox19_nse_unit_test.out
-
       - name: Compile, burn_cell_sdc (NSE, aprox19)
         run: |
           cd unit_test/burn_cell_sdc

diff --git a/CHANGES.md b/CHANGES.md
@@ -1,3 +1,54 @@
+# 24.08
+
+  * autodiff is now used with the templated reaction networks (#1614)
+    + some autodiff clean-ups and derivative fixes (#1604, #1612,
+    #1613, #1616, #1619, #1633)
+
+  * we can now output warnings from GPUs if you compile with
+    `USE_GPU_PRINTF=TRUE` (#1629, #1635)
+
+  * documentation improvements (#1570, #1628)
+
+  * a new jacobian unit (`jac_cell`) test was added that compares the
+    numerical and analytic Jacobians (#1618)
+
+  * support for Strang + NSE has been removed.  NSE only works with
+    SDC now (#1549, #1621)
+
+  * the network `CNO_He_burn` was added for explosive H/He burning
+    (#1622)
+
+  * code clean-ups (#1582, #1602, #1609, #1623, #1624, #1625, #1626,
+    #1627, #1631, #1639)
+
+  * `test_nse_net` now also tests the NSE EOS interface (#1621)
+
+  * the self-consistent NSE + SDC update has been synced with the
+    tabular NSE implementation (#1569, #1607, #1617)
+
+  * `test_jac` was not correctly evaluating the numerical Jacobian
+    (#1615)
+
+  * the `fast_atan` function is now more accurate (#1611)
+
+  * `test_ase` was renamed `test_nse_net` and the old `test_nse` was
+    removed (#1610)
+
+  * the old `test_screening` unit test was removed (#1608)
+
+  * the RKC integrator now supports NSE bailout (#1544)
+
+  * a second temperature check for tabular NSE was added -- above this
+    temperature we don't consider composition (#1547)
+
+  * a SDC+NSE unit test was added (#1548)
+
+  * a fast log and fast pow approximation was added (#1591)
+
+  * the primordial_chem network now uses the fast math routines (#1605)
+
+  * fix potential Inf in constexpr linear algebra (#1603)
+
 # 24.07
 
    * added an autodiff library and converted all of the screening

diff --git a/EOS/breakout/actual_eos.H b/EOS/breakout/actual_eos.H
@@ -8,17 +8,15 @@
 #include <network.H>
 #include <actual_eos_data.H>
 
-using namespace eos_rp;
-
 const std::string eos_name = "breakout";
 
 inline
 void actual_eos_init ()
 {
 
     // constant ratio of specific heats
-    if (eos_gamma > 0.e0_rt) {
-        gamma_const = eos_gamma;
+    if (eos_rp::eos_gamma > 0.e0_rt) {
+        gamma_const = eos_rp::eos_gamma;
     } else {
         gamma_const = 5.0_rt / 3.0_rt;
     }

diff --git a/EOS/gamma_law/actual_eos.H b/EOS/gamma_law/actual_eos.H
@@ -6,8 +6,6 @@
 #include <fundamental_constants.H>
 #include <cmath>
 
-using namespace eos_rp;
-
 // This is a constant gamma equation of state, using an ideal gas.
 //
 // The gas may either be completely ionized or completely neutral.
@@ -22,7 +20,7 @@ inline
 void actual_eos_init() {
 
   // constant ratio of specific heats
-  if (eos_gamma <= 0.0) {
+  if (eos_rp::eos_gamma <= 0.0) {
     amrex::Error("gamma_const cannot be < 0");
   }
 
@@ -56,7 +54,7 @@ void actual_eos (I input, T& state)
     const amrex::Real m_nucleon = C::m_u;
 
     if constexpr (has_xn<T>::value) {
-        if (eos_assume_neutral) {
+        if (eos_rp::eos_assume_neutral) {
             state.mu = state.abar;
         } else {
             amrex::Real sum = 0.0;
@@ -88,7 +86,7 @@ void actual_eos (I input, T& state)
         // h = e + p/rho = (p/rho)*[1 + 1/(gamma-1)] = (p/rho)*gamma/(gamma-1)
 
           if constexpr (has_enthalpy<T>::value) {
-              state.T = (state.h * state.mu * m_nucleon / C::k_B)*(eos_gamma - 1.0)/eos_gamma;
+              state.T = (state.h * state.mu * m_nucleon / C::k_B)*(eos_rp::eos_gamma - 1.0)/eos_rp::eos_gamma;
           }
 
           break;
@@ -127,7 +125,7 @@ void actual_eos (I input, T& state)
           // e = k T / [(mu m_nucleon)*(gamma-1)]
 
           if constexpr (has_energy<T>::value) {
-              state.T = state.e * state.mu * m_nucleon * (eos_gamma - 1.0) / C::k_B;
+              state.T = state.e * state.mu * m_nucleon * (eos_rp::eos_gamma - 1.0) / C::k_B;
           }
 
           break;
@@ -162,7 +160,7 @@ void actual_eos (I input, T& state)
           // Solve for temperature and density
 
           if constexpr (has_pressure<T>::value && has_enthalpy<T>::value) {
-              state.rho = state.p / state.h * eos_gamma / (eos_gamma - 1.0);
+              state.rho = state.p / state.h * eos_rp::eos_gamma / (eos_rp::eos_gamma - 1.0);
               state.T = state.p * state.mu * m_nucleon / (C::k_B * state.rho);
           }
 
@@ -199,7 +197,7 @@ void actual_eos (I input, T& state)
     // Compute the pressure simply from the ideal gas law, and the
     // specific internal energy using the gamma-law EOS relation.
     amrex::Real pressure = state.rho * state.T * C::k_B / (state.mu * m_nucleon);
-    amrex::Real energy = pressure / (eos_gamma - 1.0) * rhoinv;
+    amrex::Real energy = pressure / (eos_rp::eos_gamma - 1.0) * rhoinv;
     if constexpr (has_pressure<T>::value) {
         state.p = pressure;
     }
@@ -256,17 +254,17 @@ void actual_eos (I input, T& state)
         state.cv = state.dedT;
 
         if constexpr (has_pressure<T>::value) {
-            state.cp = eos_gamma * state.cv;
+            state.cp = eos_rp::eos_gamma * state.cv;
 
-            state.gam1 = eos_gamma;
+            state.gam1 = eos_rp::eos_gamma;
 
             state.dpdr_e = state.dpdr - state.dpdT * state.dedr * (1.0 / state.dedT);
             state.dpde = state.dpdT * (1.0 / state.dedT);
 
             // sound speed
-            state.cs = std::sqrt(eos_gamma * state.p * rhoinv);
+            state.cs = std::sqrt(eos_rp::eos_gamma * state.p * rhoinv);
             if constexpr (has_G<T>::value) {
-                state.G = 0.5 * (1.0 + eos_gamma);
+                state.G = 0.5 * (1.0 + eos_rp::eos_gamma);
             }
         }
     }
@@ -278,7 +276,7 @@ void actual_eos (I input, T& state)
         state.dedA = - state.e * (1.0 / state.abar);
     }
 
-    if (eos_assume_neutral) {
+    if (eos_rp::eos_assume_neutral) {
         if constexpr (has_dpdZ<T>::value) {
             state.dpdZ = 0.0;
         }

diff --git a/EOS/helmholtz/actual_eos.H b/EOS/helmholtz/actual_eos.H
@@ -16,8 +16,6 @@
 #include <cmath>
 #include <vector>
 
-using namespace eos_rp;
-
 // Frank Timmes Helmholtz based Equation of State
 // https://cococubed.com/
 
@@ -156,9 +154,9 @@ void apply_electrons (T& state)
 
     // hash locate this temperature and density
     int jat = int((std::log10(state.T) - tlo) * tstpi) + 1;
-    jat = amrex::max(1, amrex::min(jat, jmax-1)) - 1;
+    jat = std::clamp(jat, 1, jmax-1) - 1;
     int iat = int((std::log10(din) - dlo) * dstpi) + 1;
-    iat = amrex::max(1, amrex::min(iat, imax-1)) - 1;
+    iat = std::clamp(iat, 1, imax-1) - 1;
 
     amrex::Real fi[36];
 
@@ -576,8 +574,8 @@ void apply_radiation (T& state)
     // on prad, this will result in the radiation term effectively vanishing below the
     // cutoff density. For simplicity we ignore the effect this has on the derivatives.
 
-    if (prad_limiter_rho_c > 0.0e0_rt && prad_limiter_delta_rho > 0.0e0_rt) {
-        prad = prad * 0.5e0_rt * (1.0e0_rt + std::tanh((state.rho - prad_limiter_rho_c) / prad_limiter_delta_rho));
+    if (eos_rp::prad_limiter_rho_c > 0.0e0_rt && eos_rp::prad_limiter_delta_rho > 0.0e0_rt) {
+        prad = prad * 0.5e0_rt * (1.0e0_rt + std::tanh((state.rho - eos_rp::prad_limiter_rho_c) / eos_rp::prad_limiter_delta_rho));
     }
 
     amrex::Real dpraddd = 0.0e0_rt;
@@ -1005,7 +1003,7 @@ void single_iter_update (T& state, int var, int dvar,
     amrex::Real xnew = x - (v - v_want) / dvdx;
 
     // Don't let the temperature/density change by more than a factor of two
-    xnew = amrex::max(0.5_rt * x, amrex::min(xnew, 2.0_rt * x));
+    xnew = std::clamp(xnew, 0.5_rt * x, 2.0_rt * x);
 
     // Don't let us freeze/evacuate
     xnew = amrex::max(smallx, xnew);
@@ -1120,8 +1118,8 @@ void double_iter_update (T& state, int var1, int var2,
 
     // Don't let the temperature or density change by more
     // than a factor of two
-    tnew = amrex::max(0.5e0_rt * told, amrex::min(tnew, 2.0e0_rt * told));
-    rnew = amrex::max(0.5e0_rt * rold, amrex::min(rnew, 2.0e0_rt * rold));
+    tnew = std::clamp(tnew, 0.5e0_rt * told, 2.0e0_rt * told);
+    rnew = std::clamp(rnew, 0.5e0_rt * rold, 2.0e0_rt * rold);
 
     // Don't let us freeze or evacuate
     tnew = amrex::max(EOSData::mintemp, tnew);
@@ -1310,10 +1308,10 @@ void actual_eos_init ()
 
     // Read in the runtime parameters
 
-    input_is_constant = eos_input_is_constant;
-    do_coulomb = use_eos_coulomb;
-    ttol = eos_ttol;
-    dtol = eos_dtol;
+    input_is_constant = eos_rp::eos_input_is_constant;
+    do_coulomb = eos_rp::use_eos_coulomb;
+    ttol = eos_rp::eos_ttol;
+    dtol = eos_rp::eos_dtol;
 
     //    read the helmholtz free energy table