Merge branch 'development' into prob_params_cleaning

AMReX-Astro · Feb 10, 2024 · 7172927 · 7172927
2 parents feb54ef + 744521b
commit 7172927
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diff --git a/.clang-tidy b/.clang-tidy
@@ -7,7 +7,6 @@ Checks: >
      clang-diagnostic-*,
      cppcoreguidelines-*,
        -cppcoreguidelines-avoid-c-arrays,
-       -cppcoreguidelines-avoid-goto,
        -cppcoreguidelines-avoid-magic-numbers,
        -cppcoreguidelines-avoid-non-const-global-variables,
        -cppcoreguidelines-init-variables,
@@ -17,11 +16,17 @@ Checks: >
        -cppcoreguidelines-non-private-member-variables-in-classes,
        -cppcoreguidelines-owning-memory,
        -cppcoreguidelines-pro-*,
+     misc-*,
+       -misc-const-correctness,
+       -misc-include-cleaner,
+       -misc-non-private-member-variables-in-classes,
      modernize-*,
        -modernize-avoid-c-arrays,
        -modernize-use-trailing-return-type,
        -modernize-use-using,
      performance-*,
+       -performance-avoid-endl,
+     portability-*,
      readability-*,
        -readability-avoid-const-params-in-decls,
        -readability-braces-around-statements,

diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -0,0 +1,9 @@
+# Dependabot configuration
+# ref: https://docs.github.com/en/code-security/supply-chain-security/keeping-your-dependencies-updated-automatically/configuration-options-for-dependency-updates
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    target-branch: "development"
diff --git a/.github/workflows/c-linter.yml b/.github/workflows/c-linter.yml
@@ -30,7 +30,7 @@ jobs:
           tar xfz v2.28.0.tar.gz
           cd hypre-2.28.0/src
           ./configure --with-cxxstandard=17 --without-MPI
-          make -j 2
+          make -j 4
           make install
           cd ../../
 

diff --git a/.github/workflows/check-ifdefs.yml b/.github/workflows/check-ifdefs.yml
@@ -14,7 +14,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
 

diff --git a/.github/workflows/codespell.yml b/.github/workflows/codespell.yml
@@ -19,7 +19,7 @@ jobs:
           fetch-depth: 0
 
       - name: Setup Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: '3.10'
           cache: "pip"

diff --git a/.github/workflows/compiler-warnings.yml b/.github/workflows/compiler-warnings.yml
@@ -26,14 +26,14 @@ jobs:
       - name: Compile Detonation
         run: |
           cd Exec/science/Detonation
-          make USE_MPI=FALSE USE_OMP=FALSE DEBUG=TRUE WARN_ALL=TRUE WARN_ERROR=TRUE -j 2
+          make USE_MPI=FALSE USE_OMP=FALSE DEBUG=TRUE WARN_ALL=TRUE WARN_ERROR=TRUE -j 4
 
       - name: Compile subchandra
         run: |
           cd Exec/science/subchandra
-          make USE_MPI=FALSE USE_OMP=FALSE DEBUG=TRUE WARN_ALL=TRUE WARN_ERROR=TRUE -j 2
+          make USE_MPI=FALSE USE_OMP=FALSE DEBUG=TRUE WARN_ALL=TRUE WARN_ERROR=TRUE -j 4
 
       - name: Compile wdmerger
         run: |
           cd Exec/science/wdmerger
-          make USE_MPI=FALSE USE_OMP=FALSE DEBUG=TRUE WARN_ALL=TRUE WARN_ERROR=TRUE -j 2
+          make USE_MPI=FALSE USE_OMP=FALSE DEBUG=TRUE WARN_ALL=TRUE WARN_ERROR=TRUE -j 4
diff --git a/.github/workflows/detonation-sdc-compare.yml b/.github/workflows/detonation-sdc-compare.yml
@@ -26,7 +26,7 @@ jobs:
       - name: Compile Detonation
         run: |
           cd Exec/science/Detonation
-          make DIM=1 USE_MPI=FALSE -j 2 USE_SIMPLIFIED_SDC=TRUE
+          make DIM=1 USE_MPI=FALSE -j 4 USE_SIMPLIFIED_SDC=TRUE
 
       - name: Run Detonation
         run: |
@@ -36,7 +36,7 @@ jobs:
       - name: Build the fextrema tool
         run: |
           cd external/amrex/Tools/Plotfile
-          make programs=fextrema -j 2
+          make programs=fextrema -j 4
 
       - name: Check the extrema
         run: |

diff --git a/.github/workflows/good_defines.txt b/.github/workflows/good_defines.txt
@@ -3,6 +3,7 @@ AMREX_PARTICLES
 AMREX_SPACEDIM
 AMREX_USE_CUDA
 AMREX_USE_GPU
+AMREX_USE_HIP
 AMREX_USE_OMP
 AUX_THERMO
 BL_FORT_USE_LOWERCASE

diff --git a/.github/workflows/gpu_action.yml b/.github/workflows/gpu_action.yml
@@ -39,7 +39,7 @@ jobs:
           tar xfz v2.28.0.tar.gz
           cd hypre-2.28.0/src
           CUDA_HOME=/usr/local/cuda HYPRE_CUDA_SM=60 ./configure --with-cxxstandard=17 --with-cuda --enable-unified-memory --without-MPI
-          make -j 2
+          make -j 4
           make install
           cd ../../
 

diff --git a/.github/workflows/hip.yml b/.github/workflows/hip.yml
@@ -29,4 +29,4 @@ jobs:
       - name: compile flame_wave
         run: |
           cd Exec/science/flame_wave
-          make COMP=gnu USE_HIP=TRUE USE_MPI=FALSE USE_OMP=FALSE USE_CUDA=FALSE -j 2
+          make COMP=gnu USE_HIP=TRUE USE_MPI=FALSE USE_OMP=FALSE USE_CUDA=FALSE -j 4
diff --git a/.github/workflows/mhd-compare.yml b/.github/workflows/mhd-compare.yml
@@ -26,7 +26,7 @@ jobs:
       - name: Compile OrszagTang
         run: |
           cd Exec/mhd_tests/OrszagTang
-          make USE_MPI=TRUE -j 2
+          make USE_MPI=TRUE -j 4
 
       - name: Run OrszagTang-3d
         run: |
@@ -36,7 +36,7 @@ jobs:
       - name: Build the fextrema tool
         run: |
           cd external/amrex/Tools/Plotfile
-          make programs=fextrema -j 2
+          make programs=fextrema -j 4
 
       - name: Check the extrema
         run: |

diff --git a/.github/workflows/rad-compare.yml b/.github/workflows/rad-compare.yml
@@ -29,7 +29,7 @@ jobs:
           tar xfz v2.26.0.tar.gz
           cd hypre-2.26.0/src
           ./configure --with-cxxstandard=17
-          make -j 2
+          make -j 4
           make install
           cd ../../
 
@@ -47,7 +47,7 @@ jobs:
       - name: Build the fextrema tool
         run: |
           cd external/amrex/Tools/Plotfile
-          make programs=fextrema -j 2
+          make programs=fextrema -j 4
 
       - name: Check the extrema
         run: |

diff --git a/.github/workflows/reacting-convergence-true-sdc.yml b/.github/workflows/reacting-convergence-true-sdc.yml
@@ -26,7 +26,7 @@ jobs:
       - name: Compile reacting_convergence
         run: |
           cd Exec/reacting_tests/reacting_convergence
-          make DIM=2 USE_MPI=FALSE -j 2 USE_TRUE_SDC=TRUE
+          make DIM=2 USE_MPI=FALSE -j 4 USE_TRUE_SDC=TRUE
 
       - name: Run reacting_convergence
         run: |
@@ -36,7 +36,7 @@ jobs:
       - name: Build the fextrema tool
         run: |
           cd external/amrex/Tools/Plotfile
-          make programs=fextrema -j 2
+          make programs=fextrema -j 4
 
       - name: Check the extrema
         run: |

diff --git a/.github/workflows/uniform_cube.yml b/.github/workflows/uniform_cube.yml
@@ -26,7 +26,7 @@ jobs:
       - name: Compile uniform_cube
         run: |
           cd Exec/gravity_tests/uniform_cube
-          make USE_MPI=FALSE -j 2
+          make USE_MPI=FALSE -j 4
 
       - name: Run uniform_cube
         run: |

diff --git a/.github/workflows/uniform_sphere.yml b/.github/workflows/uniform_sphere.yml
@@ -26,7 +26,7 @@ jobs:
       - name: Compile uniform_sphere
         run: |
           cd Exec/gravity_tests/uniform_sphere
-          make USE_MPI=FALSE -j 2
+          make USE_MPI=FALSE -j 4
 
       - name: Run uniform_sphere
         run: |

diff --git a/CHANGES.md b/CHANGES.md
@@ -1,3 +1,15 @@
+# 24.02
+
+  * Lot's of code fixes from coverity and clang-tidy (#2736, #2734,
+    #2735, #2731, #2732, #2733)
+
+  * Fix the boundary condition logic at a wall for Detonation (#2722)
+
+  * Reimplement the shock detection algorithm to account for sources
+    and do a better job in multidimensions (#2711, #2710, #2709, #2704)
+
+  * Start the process of moving the runtime parameters to structs (#2688)
+
 # 24.01
 
   * An option for unlimited PPM reconstruction was added (#2670)

diff --git a/CITATION.md b/CITATION.md
@@ -29,23 +29,23 @@ provides some details on the algorithmic implementations):
 ```
     @ARTICLE{2010ApJ...715.1221A,
        author = {{Almgren}, A.~S. and {Beckner}, V.~E. and {Bell},
-		      J.~B. and {Day}, M.~S. and {Howell}, L.~H. and
-		      {Joggerst}, C.~C. and {Lijewski}, M.~J. and
-		      {Nonaka}, A. and {Singer}, M. and {Zingale}, M.},
-	title = "{CASTRO: A New Compressible Astrophysical
-		      Solver. I. Hydrodynamics and Self-gravity}",
+                      J.~B. and {Day}, M.~S. and {Howell}, L.~H. and
+                      {Joggerst}, C.~C. and {Lijewski}, M.~J. and
+                      {Nonaka}, A. and {Singer}, M. and {Zingale}, M.},
+        title = "{CASTRO: A New Compressible Astrophysical
+                      Solver. I. Hydrodynamics and Self-gravity}",
       journal = {\apj},
     archivePrefix = "arXiv",
        eprint = {1005.0114},
      primaryClass = "astro-ph.IM",
      keywords = {equation of state, gravitation, hydrodynamics, methods:
-		      numerical, nuclear reactions, nucleosynthesis,
-		      abundances},
-	 year = 2010,
-	month = jun,
+                      numerical, nuclear reactions, nucleosynthesis,
+                      abundances},
+         year = 2010,
+        month = jun,
        volume = 715,
-	pages = {1221-1238},
-	  doi = {10.1088/0004-637X/715/2/1221},
+        pages = {1221-1238},
+          doi = {10.1088/0004-637X/715/2/1221},
        adsurl = {http://adsabs.harvard.edu/abs/2010ApJ...715.1221A},
       adsnote = {Provided by the SAO/NASA Astrophysics Data System}
     }
@@ -64,21 +64,21 @@ cite the following:
 ```
     @ARTICLE{2011ApJS..196...20Z,
        author = {{Zhang}, W. and {Howell}, L. and {Almgren}, A. and
-		      {Burrows}, A. and {Bell}, J.},
-	title = "{CASTRO: A New Compressible Astrophysical
-		      Solver. II. Gray Radiation Hydrodynamics}",
+                      {Burrows}, A. and {Bell}, J.},
+        title = "{CASTRO: A New Compressible Astrophysical
+                      Solver. II. Gray Radiation Hydrodynamics}",
       journal = {\apjs},
     archivePrefix = "arXiv",
        eprint = {1105.2466},
      primaryClass = "astro-ph.IM",
      keywords = {diffusion, hydrodynamics, methods: numerical, radiative
-		      transfer},
-	 year = 2011,
-	month = oct,
+                      transfer},
+         year = 2011,
+        month = oct,
        volume = 196,
-	  eid = {20},
-	pages = {20},
-	  doi = {10.1088/0067-0049/196/2/20},
+          eid = {20},
+        pages = {20},
+          doi = {10.1088/0067-0049/196/2/20},
        adsurl = {http://adsabs.harvard.edu/abs/2011ApJS..196...20Z},
       adsnote = {Provided by the SAO/NASA Astrophysics Data System}
     }
@@ -87,21 +87,21 @@ cite the following:
 ```
     @ARTICLE{2013ApJS..204....7Z,
        author = {{Zhang}, W. and {Howell}, L. and {Almgren}, A. and
-		      {Burrows}, A. and {Dolence}, J. and {Bell}, J.},
-	title = "{CASTRO: A New Compressible Astrophysical
-		      Solver. III. Multigroup Radiation Hydrodynamics}",
+                      {Burrows}, A. and {Dolence}, J. and {Bell}, J.},
+        title = "{CASTRO: A New Compressible Astrophysical
+                      Solver. III. Multigroup Radiation Hydrodynamics}",
       journal = {\apjs},
     archivePrefix = "arXiv",
        eprint = {1207.3845},
      primaryClass = "astro-ph.IM",
      keywords = {diffusion, hydrodynamics, methods: numerical, radiative
-		      transfer },
-	 year = 2013,
-	month = jan,
+                      transfer },
+         year = 2013,
+        month = jan,
        volume = 204,
-	  eid = {7},
-	pages = {7},
-	  doi = {10.1088/0067-0049/204/1/7},
+          eid = {7},
+        pages = {7},
+          doi = {10.1088/0067-0049/204/1/7},
        adsurl = {http://adsabs.harvard.edu/abs/2013ApJS..204....7Z},
       adsnote = {Provided by the SAO/NASA Astrophysics Data System}
     }
@@ -116,22 +116,22 @@ hydro and gravity:
 ```
     @ARTICLE{2016ApJ...819...94K,
        author = {{Katz}, M.~P. and {Zingale}, M. and {Calder}, A.~C. and
-		      {Swesty}, F.~D. and {Almgren}, A.~S. and {Zhang},
-		      W.},
-	title = "{White Dwarf Mergers on Adaptive Meshes. I. Methodology
-		      and Code Verification}",
+                      {Swesty}, F.~D. and {Almgren}, A.~S. and {Zhang},
+                      W.},
+        title = "{White Dwarf Mergers on Adaptive Meshes. I. Methodology
+                      and Code Verification}",
       journal = {\apj},
     archivePrefix = "arXiv",
        eprint = {1512.06099},
      primaryClass = "astro-ph.HE",
      keywords = {hydrodynamics, methods: numerical, supernovae: general,
-		      white dwarfs},
-	 year = 2016,
-	month = mar,
+                      white dwarfs},
+         year = 2016,
+        month = mar,
        volume = 819,
-	  eid = {94},
-	pages = {94},
-	  doi = {10.3847/0004-637X/819/2/94},
+          eid = {94},
+        pages = {94},
+          doi = {10.3847/0004-637X/819/2/94},
        adsurl = {http://adsabs.harvard.edu/abs/2016ApJ...819...94K},
       adsnote = {Provided by the SAO/NASA Astrophysics Data System}
     }