Merge branch 'development' into fix_transverse_use_eos

.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/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
 

.github/workflows/dependencies_hip.sh → .github/workflows/dependencies/dependencies_hip.sh

@@ -40,6 +40,7 @@ echo 'export PATH=/opt/rocm/llvm/bin:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/r
 
 # we should not need to export HIP_PATH=/opt/rocm/hip with those installs
 
+sudo apt-get clean
 sudo apt-get update
 
 # Ref.: https://rocmdocs.amd.com/en/latest/Installation_Guide/Installation-Guide.html#installing-development-packages-for-cross-compilation
@@ -56,7 +57,9 @@ sudo apt-get install -y --no-install-recommends \
     roctracer-dev   \
     rocprofiler-dev \
     rocrand-dev     \
-    rocprim-dev
+    rocfft-dev      \
+    rocprim-dev     \
+    rocsparse-dev
 
 # hiprand-dev is a new package that does not exist in old versions
 sudo apt-get install -y --no-install-recommends hiprand-dev || true

.github/workflows/dependencies/dependencies_nvcc.sh

@@ -0,0 +1,42 @@
+#!/usr/bin/env bash
+#
+# Copyright 2020-2022 Axel Huebl
+#
+# License: BSD-3-Clause-LBNL
+
+set -eu -o pipefail
+
+# `man apt.conf`:
+#   Number of retries to perform. If this is non-zero APT will retry
+#   failed files the given number of times.
+echo 'Acquire::Retries "3";' | sudo tee /etc/apt/apt.conf.d/80-retries
+
+sudo apt-get -qqq update
+sudo apt-get install -y \
+    build-essential     \
+    ca-certificates     \
+    cmake               \
+    g++                 \
+    gfortran            \
+    gnupg               \
+    libopenmpi-dev      \
+    openmpi-bin         \
+    pkg-config          \
+    wget
+
+VERSION_DOTTED=${1-12.0} && VERSION_DASHED=$(sed 's/\./-/' <<< $VERSION_DOTTED)
+curl -O https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64/cuda-keyring_1.0-1_all.deb
+sudo dpkg -i cuda-keyring_1.0-1_all.deb
+sudo apt-get update
+sudo apt-get install -y \
+    cuda-command-line-tools-$VERSION_DASHED \
+    cuda-compiler-$VERSION_DASHED           \
+    cuda-cupti-dev-$VERSION_DASHED          \
+    cuda-minimal-build-$VERSION_DASHED      \
+    cuda-nvml-dev-$VERSION_DASHED           \
+    cuda-nvtx-$VERSION_DASHED               \
+    libcublas-dev-$VERSION_DASHED           \
+    libcufft-dev-$VERSION_DASHED            \
+    libcurand-dev-$VERSION_DASHED           \
+    libcusparse-dev-$VERSION_DASHED
+sudo ln -s cuda-$VERSION_DOTTED /usr/local/cuda

.github/workflows/gpu_action.yml

@@ -29,14 +29,7 @@ jobs:
           sudo apt-get -qq -y install curl cmake jq clang g++>=9.3.0
 
       - name: Install CUDA
-        # from https://developer.nvidia.com/cuda-downloads?target_os=Linux&target_arch=x86_64&Distribution=Ubuntu&target_version=20.04&target_type=deb_network
-        run: |
-          wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64/cuda-ubuntu2004.pin
-          sudo mv cuda-ubuntu2004.pin /etc/apt/preferences.d/cuda-repository-pin-600
-          sudo apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64/3bf863cc.pub
-          sudo add-apt-repository "deb https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64/ /"
-          sudo apt-get update
-          sudo apt-get -y install cuda-toolkit-11-8
+        run: .github/workflows/dependencies/dependencies_nvcc.sh 11.8
 
       - name: Install hypre
         run: |

.github/workflows/hip.yml

@@ -24,7 +24,7 @@ jobs:
           cd ../..
 
       - name: Dependencies
-        run: .github/workflows/dependencies_hip.sh
+        run: .github/workflows/dependencies/dependencies_hip.sh
 
       - name: compile flame_wave
         run: |

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

Docs/source/radiation.rst

@@ -126,7 +126,7 @@ frequency, and :math:`m`, :math:`n` and :math:`p` are constants. For the gray so
 
 ::
 
-    Opacity_dir := rad_power_law
+    OPACITY_DIR := rad_power_law
 
 in your GNUmakefile. See § \ `3.3.1 <#sec:opacpars>`__ for instructions on how
 to configure the parameters used for this opacity setup. If you would prefer a different

Exec/radiation_tests/Rad2Tshock/GNUmakefile

@@ -17,7 +17,7 @@ EOS_DIR     := gamma_law
 NETWORK_DIR := general_null
 NETWORK_INPUTS := gammalaw.net
 
-Opacity_dir := rad_power_law
+OPACITY_DIR := rad_power_law
 
 PROBLEM_DIR ?= ./
 

Exec/radiation_tests/RadBlastWave/GNUmakefile

@@ -15,7 +15,7 @@ EOS_DIR     := gamma_law
 NETWORK_DIR := general_null
 NETWORK_INPUTS := gammalaw.net
 
-Opacity_dir := rad_power_law
+OPACITY_DIR := rad_power_law
 
 PROBLEM_DIR ?= ./
 

Exec/radiation_tests/RadBreakout/GNUmakefile

@@ -18,7 +18,7 @@ CASTRO_HOME ?= ../../..
 EOS_DIR     = breakout
 NETWORK_DIR := general_null
 NETWORK_INPUTS = breakout.net
-Opacity_dir = breakout
+OPACITY_DIR = breakout
 
 PROBLEM_DIR ?= ./
 

Exec/radiation_tests/RadFront/GNUmakefile

@@ -17,7 +17,7 @@ EOS_DIR     := gamma_law
 NETWORK_DIR := general_null
 NETWORK_INPUTS := gammalaw.net
 
-Opacity_dir := rad_power_law
+OPACITY_DIR := rad_power_law
 
 PROBLEM_DIR ?= ./
 

Exec/radiation_tests/RadShestakovBolstad/GNUmakefile

@@ -17,7 +17,7 @@ EOS_DIR     := rad_power_law
 NETWORK_DIR := general_null
 NETWORK_INPUTS := gammalaw.net
 
-Opacity_dir := rad_power_law
+OPACITY_DIR := rad_power_law
 
 # number of radiation groups -  this needs to correspond to radiation.nGroups in
 # the inputs file

Exec/radiation_tests/RadSourceTest/GNUmakefile

@@ -20,7 +20,7 @@ EOS_DIR     := rad_power_law
 NETWORK_DIR := general_null
 NETWORK_INPUTS := gammalaw.net
 
-Opacity_dir := rad_power_law
+OPACITY_DIR := rad_power_law
 
 # use radiation interpbndry
 RAD_INTERP = TRUE

Exec/radiation_tests/RadSphere/GNUmakefile

@@ -17,7 +17,7 @@ EOS_DIR     := rad_power_law
 NETWORK_DIR := general_null
 NETWORK_INPUTS := gammalaw.net
 
-Opacity_dir := rad_power_law
+OPACITY_DIR := rad_power_law
 
 # number of radiation groups -  this needs to correspond to radiation.nGroups in
 # the inputs file

Exec/radiation_tests/RadSuOlson/GNUmakefile

@@ -16,7 +16,7 @@ EOS_DIR     := rad_power_law
 NETWORK_DIR := general_null
 NETWORK_INPUTS := gammalaw.net
 
-Opacity_dir := rad_power_law
+OPACITY_DIR := rad_power_law
 
 PROBLEM_DIR ?= ./
 

Exec/radiation_tests/RadSuOlsonMG/GNUmakefile

@@ -17,7 +17,7 @@ EOS_DIR     := rad_power_law
 NETWORK_DIR := general_null
 NETWORK_INPUTS := gammalaw.net
 
-Opacity_dir := rad_power_law
+OPACITY_DIR := rad_power_law
 
 NGROUPS := 2
 

Exec/radiation_tests/RadThermalWave/GNUmakefile

@@ -17,7 +17,7 @@ EOS_DIR     := gamma_law
 NETWORK_DIR := general_null
 NETWORK_INPUTS := gammalaw.net
 
-Opacity_dir := rad_power_law
+OPACITY_DIR := rad_power_law
 
 PROBLEM_DIR ?= ./
 

Exec/science/bwp-rad/GNUmakefile

@@ -29,7 +29,7 @@ NETWORK_DIR := general_null
 NETWORK_INPUTS := H_He.net
 
 # power-law opacity
-Opacity_dir := rad_power_law
+OPACITY_DIR := rad_power_law
 
 PROBLEM_DIR ?= ./
 

Exec/science/planet/GNUmakefile

@@ -33,7 +33,7 @@ NETWORK_DIR := general_null
 NETWORK_INPUTS := ./taeho.net
 
 # power-law opacity
-Opacity_dir := rad_power_law
+OPACITY_DIR := rad_power_law
 
 PROBLEM_DIR ?= ./
 

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
 ############################################################################################