Merge branch 'development' into new_shock_flag_call

AMReX-Astro · Apr 7, 2024 · 312d00c · 312d00c
2 parents 89e58ce + 49dcb5a
commit 312d00c
Show file tree

Hide file tree

Showing 51 changed files with 493 additions and 347 deletions.
diff --git a/.clang-tidy b/.clang-tidy
@@ -13,7 +13,6 @@ Checks: >
        -cppcoreguidelines-init-variables,
        -cppcoreguidelines-interfaces-global-init,
        -cppcoreguidelines-macro-usage,
-       -cppcoreguidelines-no-malloc,
        -cppcoreguidelines-non-private-member-variables-in-classes,
        -cppcoreguidelines-owning-memory,
        -cppcoreguidelines-pro-*,
@@ -25,7 +24,6 @@ Checks: >
      modernize-*,
        -modernize-avoid-c-arrays,
        -modernize-use-trailing-return-type,
-       -modernize-use-using,
      performance-*,
        -performance-avoid-endl,
      portability-*,

diff --git a/.github/workflows/c-linter.yml b/.github/workflows/c-linter.yml
@@ -2,6 +2,10 @@ name: cpp-linter
 
 on: [pull_request]
 
+concurrency:
+  group: ${{ github.ref }}-${{ github.head_ref }}-${{ github.workflow }}
+  cancel-in-progress: true
+
 jobs:
   cpp-linter:
     runs-on: ubuntu-latest

diff --git a/.github/workflows/check_pr_branch.yml b/.github/workflows/check_pr_branch.yml
@@ -0,0 +1,20 @@
+name: check PR branch
+
+on:
+  pull_request:
+    types:
+      - opened
+      - synchronize
+      - reopened
+      - edited
+
+jobs:
+  check-PR-branch:
+    runs-on: ubuntu-latest
+    steps:
+      - name: PRs should not target main
+        run: |
+          if [[ "${{ github.base_ref }}" == "main" ]]; then
+            echo 'Pull requests must not be made against main. Please target development instead.'
+            exit 1
+          fi
diff --git a/.github/workflows/clang-tidy.yml b/.github/workflows/clang-tidy.yml
@@ -0,0 +1,36 @@
+name: "clang-tidy"
+
+on: [pull_request]
+
+concurrency:
+  group: ${{ github.ref }}-${{ github.head_ref }}-${{ github.workflow }}
+  cancel-in-progress: true
+
+jobs:
+  clang_tidy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Get submodules
+        run: |
+          git submodule update --init
+          cd external/Microphysics
+          git fetch; git checkout development
+          echo "MICROPHYSICS_HOME=$(pwd)" >> $GITHUB_ENV
+          cd ../amrex
+          git fetch; git checkout development
+          echo "AMREX_HOME=$(pwd)" >> $GITHUB_ENV
+          cd ../..
+
+      - name: Install dependencies
+        run: |
+          .github/workflows/dependencies_clang-tidy-apt-llvm.sh 17
+
+      - 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
+
diff --git a/.github/workflows/compiler-warnings.yml b/.github/workflows/compiler-warnings.yml
@@ -1,6 +1,11 @@
 name: "compiler warnings"
 
 on: [pull_request]
+
+concurrency:
+  group: ${{ github.ref }}-${{ github.head_ref }}-${{ github.workflow }}
+  cancel-in-progress: true
+
 jobs:
   compiler_warnings:
     runs-on: ubuntu-latest

diff --git a/.github/workflows/dependencies_clang-tidy-apt-llvm.sh b/.github/workflows/dependencies_clang-tidy-apt-llvm.sh
@@ -0,0 +1,22 @@
+#!/usr/bin/env bash
+
+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
+
+if [[ ! -f /etc/apt/trusted.gpg.d/apt.llvm.org.asc ]]; then
+    wget -qO- https://apt.llvm.org/llvm-snapshot.gpg.key | sudo tee /etc/apt/trusted.gpg.d/apt.llvm.org.asc
+fi
+
+source /etc/os-release # set UBUNTU_CODENAME
+
+sudo add-apt-repository "deb http://apt.llvm.org/${UBUNTU_CODENAME}/ llvm-toolchain-${UBUNTU_CODENAME} main"
+sudo add-apt-repository "deb http://apt.llvm.org/${UBUNTU_CODENAME}/ llvm-toolchain-${UBUNTU_CODENAME}-$1 main"
+
+sudo apt-get update
+
+sudo apt-get install -y --no-install-recommends \
+    clang-tidy-$1 libomp-$1-dev
diff --git a/.github/workflows/detonation-sdc-compare.yml b/.github/workflows/detonation-sdc-compare.yml
@@ -1,6 +1,11 @@
 name: detonation-sdc
 
 on: [pull_request]
+
+concurrency:
+  group: ${{ github.ref }}-${{ github.head_ref }}-${{ github.workflow }}
+  cancel-in-progress: true
+
 jobs:
   detonation-sdc:
     runs-on: ubuntu-latest

diff --git a/.github/workflows/flame_wave-compare.yml b/.github/workflows/flame_wave-compare.yml
@@ -1,6 +1,11 @@
 name: flame_wave
 
 on: [pull_request]
+
+concurrency:
+  group: ${{ github.ref }}-${{ github.head_ref }}-${{ github.workflow }}
+  cancel-in-progress: true
+
 jobs:
   flame_wave-2d:
     runs-on: ubuntu-latest

diff --git a/.github/workflows/gpu_action.yml b/.github/workflows/gpu_action.yml
@@ -1,6 +1,11 @@
 name: GPU compilation
 
 on: [pull_request]
+
+concurrency:
+  group: ${{ github.ref }}-${{ github.head_ref }}-${{ github.workflow }}
+  cancel-in-progress: true
+
 jobs:
   gpu-compilation:
     runs-on: ubuntu-latest

diff --git a/.github/workflows/wdmerger_collision-compare.yml b/.github/workflows/wdmerger_collision-compare.yml
@@ -1,6 +1,11 @@
 name: wdmerger_collision
 
 on: [pull_request]
+
+concurrency:
+  group: ${{ github.ref }}-${{ github.head_ref }}-${{ github.workflow }}
+  cancel-in-progress: true
+
 jobs:
   wdmerger_collision-2d:
     runs-on: ubuntu-latest

diff --git a/CHANGES.md b/CHANGES.md
@@ -1,3 +1,20 @@
+# 24.04
+
+  * Some clang-tidy fixes (#2779, #2780, #2781, #2784, #2786, #2787, #2790,
+    #2791, #2792, #2793, #2797, #2798, #2799, #2800, #2801, #2804)
+
+  * Fix species initialization in the Detonation problem (#2806)
+    and let it work with NSE (#2765)
+
+  * Sync up with AMReX changes (#2794)
+
+  * wdmerger now reports composition of initial stars (#2767)
+
+  * flame_wave now checks if the `atm_delta` is too small (#2782)
+    and stores X(ash) (#2773)
+
+  * a bounds issue in the true SDC integration was fixed (#2775)
+
 # 24.03
 
   * Documentation updates (#2742, #2752, #2753)

diff --git a/Docs/source/io.rst b/Docs/source/io.rst
@@ -304,6 +304,8 @@ Derived variables
 +-----------------------------------+---------------------------------------------------+-----------------------------+-----------------------------------------+
 | variable name                     | description                                       | derive routine              | units                                   |
 +===================================+===================================================+=============================+=========================================+
+| ``abar``                          | Mean atomic mass                                  | ``derabar``                 | :math:`\amu`                            |
++-----------------------------------+---------------------------------------------------+-----------------------------+-----------------------------------------+
 | ``angular_momentum_x``,           | Angular momentum / volume in the x, y, or z dir   | ``derangmomx``,             | :math:`{\rm g~cm^{-1}~s^{-1}}`          |
 | ``angular_momentum_y``,           | computed as :math:`[(\rho \ub) \times {\bf r}]_n` | ``derangmomy``,             |                                         |
 | ``angular_momentum_z``            | where :math:`{\bf r}` is the distance from        | ``derangmomz``              |                                         |
@@ -328,6 +330,8 @@ Derived variables
 |                                   | :math:`s = s(\rho, e, X_k)`, where `e` is         |                             |                                         |
 |                                   | computed from :math:`(\rho e)`                    |                             |                                         |
 +-----------------------------------+---------------------------------------------------+-----------------------------+-----------------------------------------+
+| ``enuc``                          | Nuclear energy generation rate / gram             | ``derenuc``                 | :math:`{\rm erg~g^{-1}~s^{-1}}`         |
++-----------------------------------+---------------------------------------------------+-----------------------------+-----------------------------------------+
 | ``Ertot``                         | Total radiation energy density                    | ``derertot``                |                                         |
 |                                   | (for multigroup radiation problems)               |                             |                                         |
 +-----------------------------------+---------------------------------------------------+-----------------------------+-----------------------------------------+
@@ -391,8 +395,6 @@ Derived variables
 | ``y_velocity``,                   | :math:`\ub = (\rho \ub)/\rho`                     |                             |                                         |
 | ``z_velocity``                    |                                                   |                             |                                         |
 +-----------------------------------+---------------------------------------------------+-----------------------------+-----------------------------------------+
-| ``enuc``                          | Nuclear energy generation rate / gram             | ``derenuc``                 | :math:`{\rm erg~g^{-1}~s^{-1}}`         |
-+-----------------------------------+---------------------------------------------------+-----------------------------+-----------------------------------------+
 
 problem-specific plotfile variables
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

diff --git a/Exec/Make.Castro b/Exec/Make.Castro
@@ -357,7 +357,7 @@ include $(AMREX_HOME)/Tools/GNUMake/Make.rules
 clean::
 	$(SILENT) $(RM) extern.F90 prob_params_auto.F90 extern_parameters.H extern_parameters_F.H extern_parameters.cpp
 	$(SILENT) $(RM) AMReX_buildInfo.cpp
-	$(SILENT) $(RM) $(CASTRO_AUTO_SOURCE_DIR)/*.H $(CASTRO_AUTO_SOURCE_DIR)/*.[fF]90
+	$(SILENT) $(RM) $(CASTRO_AUTO_SOURCE_DIR)/*.H $(CASTRO_AUTO_SOURCE_DIR)/*.[fF]90 $(CASTRO_AUTO_SOURCE_DIR)/*.cpp
 
 # these files are now created directly in the CASTRO_AUTO_SOURCE_DIR so eventually we
 # can get rid of explicitly removing them (this is for backwards compatibility)

diff --git a/Exec/Make.auto_source b/Exec/Make.auto_source
@@ -67,6 +67,8 @@ AUTO_BUILD_SOURCES += $(CASTRO_AUTO_SOURCE_DIR)/castro_params.H
 
 CPP_PARAMETERS := $(TOP)/Source/driver/_cpp_parameters
 
+$(CASTRO_AUTO_SOURCE_DIR)/runtime_params.cpp: $(CASTRO_AUTO_SOURCE_DIR)/castro_params.H
+
 $(CASTRO_AUTO_SOURCE_DIR)/castro_params.H: $(CPP_PARAMETERS)
 	@if [ ! -d $(CASTRO_AUTO_SOURCE_DIR) ]; then mkdir -p $(CASTRO_AUTO_SOURCE_DIR); fi
 	PYTHONPATH=$(MICROPHYSICS_HOME)/util/build_scripts $(TOP)/Source/driver/parse_castro_params.py -o $(CASTRO_AUTO_SOURCE_DIR) $(CPP_PARAMETERS)

diff --git a/Exec/hydro_tests/Sedov/problem_initialize.H b/Exec/hydro_tests/Sedov/problem_initialize.H
@@ -22,10 +22,7 @@ void problem_initialize ()
         }
     }
 
-    Real xn_zone[NumSpec];
-    for (int n = 0; n < NumSpec; ++n) {
-        xn_zone[n] = 0.0_rt;
-    }
+    Real xn_zone[NumSpec] = {0.0};
     xn_zone[0] = 1.0_rt;
 
     eos_t eos_state;
@@ -96,17 +93,20 @@ void problem_initialize ()
         vctr = (4.0_rt / 3.0_rt) * M_PI * problem::r_init * problem::r_init * problem::r_init;
 
 #else
-
         amrex::Abort("Sedov problem unsupported in 3D axisymmetric geometry.");
-
 #endif
 
     }
     else if (coord_type == 2) {
 
+
+#if AMREX_SPACEDIM == 1
         // Must have AMREX_SPACEDIM == 1 for this coord_type.
 
         vctr = (4.0_rt / 3.0_rt) * M_PI * problem::r_init * problem::r_init * problem::r_init;
+#else
+        amrex::Abort("Sedov problem unsupported in 2-D or 3-D spherical geometry.");
+#endif
 
     }