Merge branch 'development' into 2d_spherical_rotation

.clang-tidy

@@ -19,6 +19,7 @@ Checks: >
      misc-*,
        -misc-const-correctness,
        -misc-include-cleaner,
+       -misc-use-internal-linkage,
        -misc-non-private-member-variables-in-classes,
        -misc-no-recursion,
      modernize-*,
@@ -32,12 +33,14 @@ 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-redundant-inline-specifier,
        -readability-redundant-member-init,

.github/workflows/clang-tidy.yml

@@ -25,12 +25,12 @@ 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 flame_wave
         run: |
           echo $AMREX_HOME
           echo $MICROPHYSICS_HOME
           cd Exec/science/subchandra
-          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
 

CHANGES.md

@@ -1,3 +1,29 @@
+# 24.12
+
+  * update clang-tidy CI (#2992, #3002)
+
+  * fix `problo` != 0 in non-Cartesian coords (#3001)
+
+  * fix `apply_av` in spherical (#3000)
+
+  * update `xrb_spherical` analysis (#2999)
+
+  * add spherical support to plm (#2996, #2997)
+
+  * fix coverity issue (#2998)
+
+  * fix geometric source term in ppm tracing for spherical (#2995)
+
+  * fix dloga for non-radial direction in tracing (#2994)
+
+  * fix `scale_flux` in 1d for Cartesian (#2991)
+
+  * add the `xrb_spherical` problem setup (#2972)
+
+  * add a new distance function that works for all geometries (#2990)
+
+  * fix confusing geom name in derive (#2989)
+
 # 24.11
 
   * a new well-balanced method was added to the CTU PPM solver.  This

Exec/science/wdmerger/tests/he_double_det/inputs_pakmor_simp_sdc

@@ -61,7 +61,7 @@ castro.hi_bc = 2 2 2
 max_step = 10000000
 
 # Simulation end time
-stop_time = 200.0
+stop_time = 1000.0
 
 # CFL number for hyperbolic system
 castro.cfl = 0.5
@@ -70,10 +70,10 @@ castro.cfl = 0.5
 castro.fixed_dt = -1.0
 
 # Scale back initial timestep by this factor
-castro.init_shrink = 0.01
+castro.init_shrink = 0.1
 
 # Factor by which dt is allowed to change each timestep
-castro.change_max = 1.10
+castro.change_max = 1.20
 
 # If we regrid on Level 0, compute a new timestep afterward
 amr.compute_new_dt_on_regrid = 1
@@ -91,6 +91,8 @@ castro.abundance_failure_rho_cutoff = 1.0e0
 # Default is 10, 16 is recommended value
 castro.max_subcycles = 16
 
+# Switching to simplified SDC
+castro.time_integration_method = 3
 
 ############################################################################################
 # Resolution, gridding and AMR
@@ -292,20 +294,20 @@ integrator.atol_spec = 1.0e-6
 integrator.rtol_enuc = 1.0e-6
 integrator.atol_enuc = 1.0e-6
 
-# Do not abort or retry on a failed burn (Castro will handle this)
-integrator.abort_on_failure = 0
-
 # Renormalize abundances during the burn
 integrator.renormalize_abundances = 1
 
 # Maximum temperature allowed in the burn
 integrator.MAX_TEMP = 1.0e10
 
 # Use tabular rate evaluation when available
-network.use_tables = 1
+network.use_tables = 0
 
-# Switching to simplified SDC
-castro.time_integration_method = 3
+# use retry in the burner and cap the number of steps to make the
+# reactions go faster
+integrator.use_burn_retry = 1
+integrator.retry_swap_jacobian = 1
+integrator.ode_max_steps = 10000
 
 ############################################################################################
 # Gravity
@@ -380,16 +382,16 @@ amr.check_file = chk
 castro.dump_old = 1
 
 # Simulation time between checkpoints
-amr.check_per = 1.0
+amr.check_per = -1
 
 # Number of timesteps between checkpoints
-amr.check_int = -1
+amr.check_int = 50
 
 # Root name of plot files
 amr.plot_file = plt
 
 # Simulation time between plotfiles
-amr.plot_per = 1.0
+amr.plot_per = 2.0
 
 # Number of timesteps between plotfiles
 amr.plot_int = -1
@@ -426,17 +428,20 @@ gravity.v = 1
 amr.plot_vars = ALL
 
 # Derived variables to add to plot files
-amr.derive_plot_vars = pressure
+amr.derive_plot_vars = ALL
 
 # State variables to add to small plot files
 amr.small_plot_vars = density Temp
 
 # Derived variables to add to small plot files
-amr.derive_small_plot_vars = enuc X(He4) X(C12) X(O16)
+amr.derive_small_plot_vars = abar enuc MachNumber magvel magvort X(He4) X(C12) X(O16)
 
 # Name of the diagnostic sum output files
 amr.data_log = star_diag.out primary_diag.out secondary_diag.out rotation_diag.out
 
+# write plotfiles as single precision
+fab.format = NATIVE_32
+
 ############################################################################################
 # Problem parameters
 ############################################################################################

Exec/science/wdmerger/tests/he_double_det/inputs_pakmor_strang

@@ -292,17 +292,20 @@ integrator.atol_spec = 1.0e-6
 integrator.rtol_enuc = 1.0e-6
 integrator.atol_enuc = 1.0e-6
 
-# Do not abort or retry on a failed burn (Castro will handle this)
-integrator.abort_on_failure = 0
-
 # Renormalize abundances during the burn
 integrator.renormalize_abundances = 1
 
 # Maximum temperature allowed in the burn
 integrator.MAX_TEMP = 1.0e10
 
 # Use tabular rate evaluation when available
-network.use_tables = 1
+network.use_tables = 0
+
+# use retry in the burner and cap the number of steps to make the
+# reactions go faster
+integrator.use_burn_retry = 1
+integrator.retry_swap_jacobian = 1
+integrator.ode_max_steps = 10000
 
 ############################################################################################
 # Gravity
@@ -377,16 +380,16 @@ amr.check_file = chk
 castro.dump_old = 1
 
 # Simulation time between checkpoints
-amr.check_per = 1.0
+amr.check_per = -1
 
 # Number of timesteps between checkpoints
-amr.check_int = -1
+amr.check_int = 50
 
 # Root name of plot files
 amr.plot_file = plt
 
 # Simulation time between plotfiles
-amr.plot_per = 1.0
+amr.plot_per = 2.0
 
 # Number of timesteps between plotfiles
 amr.plot_int = -1
@@ -423,17 +426,20 @@ gravity.v = 1
 amr.plot_vars = ALL
 
 # Derived variables to add to plot files
-amr.derive_plot_vars = pressure
+amr.derive_plot_vars = ALL
 
 # State variables to add to small plot files
 amr.small_plot_vars = density Temp
 
 # Derived variables to add to small plot files
-amr.derive_small_plot_vars = enuc X(He4) X(C12) X(O16)
+amr.derive_small_plot_vars = abar enuc MachNumber magvel magvort X(He4) X(C12) X(O16)
 
 # Name of the diagnostic sum output files
 amr.data_log = star_diag.out primary_diag.out secondary_diag.out rotation_diag.out
 
+# write plotfiles as single precision
+fab.format = NATIVE_32
+
 ############################################################################################
 # Problem parameters
 ############################################################################################

Exec/science/xrb_spherical/analysis/slice.py

@@ -66,12 +66,12 @@ def slice(fname:str, field:str,
     if field in ["x_velocity", "y_velocity", "z_velocity"]:
         sp.set_cmap(field, "coolwarm")
     elif field == "Temp":
-        sp.set_zlim(f, 5.e7, 2.5e9)
-        sp.set_cmap(f, "magma_r")
+        sp.set_zlim(field, 5.e7, 2.5e9)
+        sp.set_cmap(field, "magma_r")
     elif field == "enuc":
-        sp.set_zlim(f, 1.e18, 1.e20)
+        sp.set_zlim(field, 1.e18, 1.e20)
     elif field == "density":
-        sp.set_zlim(f, 1.e-3, 5.e8)
+        sp.set_zlim(field, 1.e-3, 5.e8)
 
     # sp.annotate_text((0.05, 0.05), f"{currentTime.in_cgs():8.5f} s")
     sp.save(f"{ds}_{loc}")

Source/driver/Castro.cpp

@@ -851,12 +851,13 @@ Castro::buildMetrics ()
         dLogArea[dir].clear();
         geom.GetDLogA(dLogArea[dir],grids,dmap,dir,NUM_GROW);
     }
-    for (int dir = AMREX_SPACEDIM; dir < 2; dir++)
-    {
-        dLogArea[dir].clear();
-        dLogArea[dir].define(grids, dmap, 1, 0);
-        dLogArea[dir].setVal(0.0);
-    }
+
+#if (AMREX_SPACEDIM == 1)
+    dLogArea[1].clear();
+    dLogArea[1].define(grids, dmap, 1, 0);
+    dLogArea[1].setVal(0.0);
+#endif
+
 #endif
 
     wall_time_start = 0.0;

Source/driver/Castro_util.H

@@ -217,7 +217,7 @@ Real volume(const int& i, const int& j, const int& k,
         Real rl = geomdata.ProbLo()[0] + static_cast<Real>(i) * dx[0];
         Real rr = rl + dx[0];
 
-        vol = M_PI * dx[0] * (rr + rl);
+        vol = std::abs(M_PI * dx[0] * (rr + rl));
 
    } else {
 
@@ -226,7 +226,7 @@ Real volume(const int& i, const int& j, const int& k,
         Real rl = geomdata.ProbLo()[0] + static_cast<Real>(i) * dx[0];
         Real rr = rl + dx[0];
 
-        vol = (4.0_rt / 3.0_rt) * M_PI * dx[0] * (rl * rl + rl * rr + rr * rr);
+        vol = std::abs((4.0_rt / 3.0_rt) * M_PI * dx[0] * (rl * rl + rl * rr + rr * rr));
 
     }
 
@@ -247,7 +247,7 @@ Real volume(const int& i, const int& j, const int& k,
         Real r_l = geomdata.ProbLo()[0] + static_cast<Real>(i) * dx[0];
         Real r_r = geomdata.ProbLo()[0] + static_cast<Real>(i+1) * dx[0];
 
-        vol = M_PI * (r_l + r_r) * dx[0] * dx[1];
+        vol = std::abs(M_PI * (r_l + r_r) * dx[0] * dx[1]);
 
     } else {
 
@@ -260,8 +260,8 @@ Real volume(const int& i, const int& j, const int& k,
         Real theta_l = geomdata.ProbLo()[1] + static_cast<Real>(j) * dx[1];
         Real theta_r = geomdata.ProbLo()[1] + static_cast<Real>(j+1) * dx[1];
 
-        vol = twoThirdsPi * (std::cos(theta_l) - std::cos(theta_r)) * dx[0] *
-            (r_r * r_r + r_r * r_l + r_l * r_l);
+        vol = std::abs(twoThirdsPi * (std::cos(theta_l) - std::cos(theta_r)) * dx[0] *
+                       (r_r * r_r + r_r * r_l + r_l * r_l));
 
     }
 
@@ -306,15 +306,15 @@ Real area(const int& i, const int& j, const int& k,
 
         Real r = geomdata.ProbLo()[0] + static_cast<Real>(i) * dx[0];
 
-        a = 2.0_rt * M_PI * r;
+        a = std::abs(2.0_rt * M_PI * r);
 
     } else {
 
         // Spherical
 
         Real r = geomdata.ProbLo()[0] + static_cast<Real>(i) * dx[0];
 
-        a = 4.0_rt * M_PI * r * r;
+        a = std::abs(4.0_rt * M_PI * r * r);
 
     }
 
@@ -339,11 +339,11 @@ Real area(const int& i, const int& j, const int& k,
 
         if (idir == 0) {
             Real r = geomdata.ProbLo()[0] + static_cast<Real>(i) * dx[0];
-            a = 2.0_rt * M_PI * r * dx[1];
+            a = std::abs(2.0_rt * M_PI * r * dx[1]);
         }
         else {
             Real r = geomdata.ProbLo()[0] + (static_cast<Real>(i) + 0.5_rt) * dx[0];
-            a = 2.0_rt * M_PI * r * dx[0];
+            a = std::abs(2.0_rt * M_PI * r * dx[0]);
         }
 
     } else {
@@ -355,13 +355,13 @@ Real area(const int& i, const int& j, const int& k,
             Real theta_l = geomdata.ProbLo()[1] + static_cast<Real>(j) * dx[1];
             Real theta_r = geomdata.ProbLo()[1] + static_cast<Real>(j+1) * dx[1];
 
-            a = 2.0_rt * M_PI * r * r * (std::cos(theta_l) - std::cos(theta_r));
+            a = std::abs(2.0_rt * M_PI * r * r * (std::cos(theta_l) - std::cos(theta_r)));
         }
         else {
             Real r = geomdata.ProbLo()[0] + (static_cast<Real>(i) + 0.5_rt) * dx[0];
             Real theta = geomdata.ProbLo()[1] + static_cast<Real>(j) * dx[1];
 
-            a = 2.0_rt * M_PI * std::sin(theta) * r * dx[0];
+            a = std::abs(2.0_rt * M_PI * std::sin(theta) * r * dx[0]);
         }
 
     }