Merge branch 'development' into detonation_nse_net_input

.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,

.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
 

.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"

.github/workflows/docs-test.yml

@@ -9,6 +9,10 @@ on:
     branches:
       - development
 
+env:
+  # enable color output from Sphinx
+  FORCE_COLOR: "1"
+
 jobs:
   docs:
     runs-on: ubuntu-latest
@@ -33,7 +37,10 @@ jobs:
       - name: Build docs
         run: |
           cd Docs/
-          make SPHINXOPTS=-v NO_DOXYGEN=TRUE html
+          # remove missing TOC entries that would otherwise be generated by
+          # doxygen to avoid warnings about missing references
+          sed -i -e 's/^   filelist$//; s/^   classlist$//' source/index.rst
+          make SPHINXOPTS='-v -W --keep-going' NO_DOXYGEN=TRUE html
 
       - name: Check links
         run: |

.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

.gitignore

@@ -72,6 +72,8 @@ Docs/source/namespacelist.rst
 Docs/source/runtime_parameters.rst
 Docs/source/*_files.rst
 Docs/source/preprocessed_files
+Docs/source/yt_example.rst
+Docs/source/yt_example_files/
 
 
 amr_diag.out

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)

Diagnostics/DustCollapse/main.cpp

@@ -102,18 +102,18 @@ int main(int argc, char* argv[])
 #if (AMREX_SPACEDIM == 1)
         int nbins = domain.length(0);
 #elif (AMREX_SPACEDIM == 2)
-        auto x_maxdist = fmax(fabs(problo[0]), fabs(probhi[0]));
-        auto y_maxdist = fmax(fabs(problo[1] - yctr), fabs(probhi[1] - yctr));
+        auto x_maxdist = std::max(std::abs(problo[0]), std::abs(probhi[0]));
+        auto y_maxdist = std::max(std::abs(problo[1] - yctr), std::abs(probhi[1] - yctr));
 
-        auto max_dist = sqrt(x_maxdist*x_maxdist + y_maxdist*y_maxdist);
+        auto max_dist = std::sqrt(x_maxdist*x_maxdist + y_maxdist*y_maxdist);
 
         int nbins = int(max_dist / dx_fine);
 #else
-        auto x_maxdist = fmax(fabs(problo[0] - xctr), fabs(probhi[0] - xctr));
-        auto y_maxdist = fmax(fabs(problo[1] - yctr), fabs(probhi[1] - yctr));
-        auto z_maxdist = fmax(fabs(problo[2] - zctr), fabs(probhi[2] - zctr));
+        auto x_maxdist = std::max(std::abs(problo[0] - xctr), std::abs(probhi[0] - xctr));
+        auto y_maxdist = std::max(std::abs(problo[1] - yctr), std::abs(probhi[1] - yctr));
+        auto z_maxdist = std::max(std::abs(problo[2] - zctr), std::abs(probhi[2] - zctr));
 
-        auto max_dist = sqrt(x_maxdist*x_maxdist + y_maxdist*y_maxdist +
+        auto max_dist = std::sqrt(x_maxdist*x_maxdist + y_maxdist*y_maxdist +
                              z_maxdist*z_maxdist);
 
         int nbins = int(max_dist / dx_fine);
@@ -147,7 +147,7 @@ int main(int argc, char* argv[])
         // over levels, we will compare to the finest level index space to
         // determine if we've already output here
         int mask_size = domain.length().max();
-        Vector<int> imask(pow(mask_size, AMREX_SPACEDIM), 1);
+        Vector<int> imask(std::pow(mask_size, AMREX_SPACEDIM), 1);
 
         // counter
         int cnt = 0;
@@ -172,17 +172,17 @@ int main(int argc, char* argv[])
                 const Box& bx = mfi.tilebox();
 
 #if (AMREX_SPACEDIM == 1)
-                fdustcollapse1d(ARLIM_3D(bx.loVect()), ARLIM_3D(bx.hiVect()),
+                fdustcollapse1d(AMREX_ARLIM_3D(bx.loVect()), AMREX_ARLIM_3D(bx.hiVect()),
                                 BL_TO_FORTRAN_FAB(lev_data_mf[mfi]),
                                 nbins, dens.dataPtr(),
                                 imask.dataPtr(), mask_size, r1, dens_comp, &cnt);
 #elif (AMREX_SPACEDIM == 2)
 
-                fdustcollapse2d(ARLIM_3D(bx.loVect()), ARLIM_3D(bx.hiVect()),
+                fdustcollapse2d(AMREX_ARLIM_3D(bx.loVect()), AMREX_ARLIM_3D(bx.hiVect()),
                                 BL_TO_FORTRAN_FAB(lev_data_mf[mfi]),
                                 nbins, dens.dataPtr(), volcount.dataPtr(),
                                 imask.dataPtr(), mask_size, r1,
-                                ZFILL(level_dx), dx_fine, yctr, dens_comp);
+                                AMREX_ZFILL(level_dx), dx_fine, yctr, dens_comp);
 #else
                 fdustcollapse3d(bx.loVect(), bx.hiVect(),
                                 BL_TO_FORTRAN_FAB(lev_data_mf[mfi]),
@@ -210,21 +210,21 @@ int main(int argc, char* argv[])
         // analytic expression for the radius as a function of time t = 0.00
         Real max_dens = 1.e9;
 
-        if (fabs(data.Time()) <= 1.e-8)
+        if (std::abs(data.Time()) <= 1.e-8)
             max_dens = 1.e9;
-        else if (fabs(data.Time() - 0.01) <= 1.e-8)
+        else if (std::abs(data.Time() - 0.01) <= 1.e-8)
             max_dens = 1.043345e9;
-        else if (fabs(data.Time() - 0.02) <= 1.e-8)
+        else if (std::abs(data.Time() - 0.02) <= 1.e-8)
             max_dens = 1.192524e9;
-        else if (fabs(data.Time() - 0.03) <= 1.e-8)
+        else if (std::abs(data.Time() - 0.03) <= 1.e-8)
             max_dens = 1.527201e9;
-        else if (fabs(data.Time() - 0.04) <= 1.e-8)
+        else if (std::abs(data.Time() - 0.04) <= 1.e-8)
             max_dens = 2.312884e9;
-        else if (fabs(data.Time() - 0.05) <= 1.e-8)
+        else if (std::abs(data.Time() - 0.05) <= 1.e-8)
             max_dens = 4.779133e9;
-        else if (fabs(data.Time() - 0.06) <= 1.e-8)
+        else if (std::abs(data.Time() - 0.06) <= 1.e-8)
             max_dens = 24.472425e9;
-        else if (fabs(data.Time() - 0.065) <= 1.e-8)
+        else if (std::abs(data.Time() - 0.065) <= 1.e-8)
             max_dens = 423.447291e9;
         else {
             Print() << "Dont know the maximum density at this time: " << data.Time() <<std::endl;

Diagnostics/Radiation/Radiation_utils.H

@@ -126,7 +126,7 @@ void WriteSlicefile(const int nbins, const Vector<Real> r,
         slicefile << std::setw(w) << r[i];
 
         for (auto it=vars.begin(); it!=vars.end(); ++it) {
-            if(fabs((*it)[i]) < SMALL) (*it)[i] = 0.0;
+            if(std::abs((*it)[i]) < SMALL) (*it)[i] = 0.0;
             slicefile << std::setw(w) << (*it)[i];
         }
 

Diagnostics/Radiation/gaussian_pulse.cpp

@@ -64,9 +64,9 @@ int main(int argc, char* argv[])
 
     // compute the size of the radially-binned array -- we'll do it to
     // the furtherest corner of the domain
-    double x_maxdist = max(fabs(probhi[0] - xctr), fabs(problo[0] - xctr));
-    double y_maxdist = max(fabs(probhi[1] - yctr), fabs(problo[1] - yctr));
-    double maxdist = sqrt(x_maxdist*x_maxdist + y_maxdist*y_maxdist);
+    double x_maxdist = std::max(std::abs(probhi[0] - xctr), std::abs(problo[0] - xctr));
+    double y_maxdist = std::max(std::abs(probhi[1] - yctr), std::abs(problo[1] - yctr));
+    double maxdist = std::sqrt(x_maxdist*x_maxdist + y_maxdist*y_maxdist);
 
     double dx_fine = *(std::min_element(dx.begin(), dx.end()));
 
@@ -102,7 +102,7 @@ int main(int argc, char* argv[])
     // over levels, we will compare to the finest level index space to
     // determine if we've already output here
     int mask_size = domain.length().max();
-    Vector<int> imask(pow(mask_size, AMREX_SPACEDIM), 1);
+    Vector<int> imask(std::pow(mask_size, AMREX_SPACEDIM), 1);
 
     // loop over the data, starting at the finest grid, and if we haven't
     // already stored data in that grid location (according to imask),
@@ -123,11 +123,11 @@ int main(int argc, char* argv[])
         for (MFIter mfi(lev_data_mf, true); mfi.isValid(); ++mfi) {
             const Box& bx = mfi.tilebox();
 
-            fgaussian_pulse(ARLIM_3D(bx.loVect()), ARLIM_3D(bx.hiVect()),
+            fgaussian_pulse(AMREX_ARLIM_3D(bx.loVect()), AMREX_ARLIM_3D(bx.hiVect()),
                             BL_TO_FORTRAN_FAB(lev_data_mf[mfi]),
                             nbins, rad_bin.dataPtr(), ncount.dataPtr(),
                             imask.dataPtr(), mask_size, r1,
-                            rad_comp, ZFILL(dx), dx_fine, xctr, yctr);
+                            rad_comp, AMREX_ZFILL(dx), dx_fine, xctr, yctr);
 
         }
 

Diagnostics/Radiation/lgt_frnt1d.cpp

@@ -53,7 +53,7 @@ int main(int argc, char* argv[])
 
     // compute the size of the radially-binned array -- we'll do it to
     // the furtherest corner of the domain
-    double maxdist = fabs(probhi[0] - problo[0]);
+    double maxdist = std::abs(probhi[0] - problo[0]);
     double dx_fine = *(std::min_element(dx.begin(), dx.end()));
     int nbins = int(maxdist / dx_fine);
 
@@ -93,7 +93,7 @@ int main(int argc, char* argv[])
     // over levels, we will compare to the finest level index space to
     // determine if we've already output here
     int mask_size = domain.length().max();
-    Vector<int> imask(pow(mask_size, AMREX_SPACEDIM), 1);
+    Vector<int> imask(std::pow(mask_size, AMREX_SPACEDIM), 1);
 
     // loop over the data, starting at the finest grid, and if we haven't
     // already stored data in that grid location (according to imask),
@@ -114,13 +114,13 @@ int main(int argc, char* argv[])
         for (MFIter mfi(lev_data_mf, true); mfi.isValid(); ++mfi) {
             const Box& bx = mfi.tilebox();
 
-            flgt_frnt1d(ARLIM_3D(bx.loVect()), ARLIM_3D(bx.hiVect()),
+            flgt_frnt1d(AMREX_ARLIM_3D(bx.loVect()), AMREX_ARLIM_3D(bx.hiVect()),
                         BL_TO_FORTRAN_FAB(lev_data_mf[mfi]),
                         nbins, dens_bin.dataPtr(), vel_bin.dataPtr(),
                         pres_bin.dataPtr(), rad_bin.dataPtr(),
                         imask.dataPtr(), mask_size, r1,
                         dens_comp, xmom_comp, pres_comp, rad_comp,
-                        ZFILL(dx), dx_fine);
+                        AMREX_ZFILL(dx), dx_fine);
         }
 
         // adjust r1 for the next lowest level

Diagnostics/Radiation/rad_shock.cpp

@@ -106,7 +106,7 @@ int main(int argc, char* argv[])
     // over levels, we will compare to the finest level index space to
     // determine if we've already output here
     int mask_size = domain.length().max();
-    Vector<int> imask(pow(mask_size, AMREX_SPACEDIM), 1);
+    Vector<int> imask(std::pow(mask_size, AMREX_SPACEDIM), 1);
 
     // counter
     auto cnt = 0;
@@ -135,7 +135,7 @@ int main(int argc, char* argv[])
         for (MFIter mfi(lev_data_mf, true); mfi.isValid(); ++mfi) {
             const Box& bx = mfi.tilebox();
 
-            fradshock(ARLIM_3D(bx.loVect()), ARLIM_3D(bx.hiVect()),
+            fradshock(AMREX_ARLIM_3D(bx.loVect()), AMREX_ARLIM_3D(bx.hiVect()),
                       problo.dataPtr(), probhi.dataPtr(),
                       BL_TO_FORTRAN_FAB(lev_data_mf[mfi]),
                       nbins, vars_bin.dataPtr(),
@@ -214,7 +214,7 @@ int main(int argc, char* argv[])
             slicefile << std::setw(w) << vars_bin[isv[i]+((*it)+1)*nbins];
 
         auto it = comps.end()-1;
-        slicefile << std::setw(w) << pow(vars_bin[isv[i]+((*it)+1)*nbins] / arad, 0.25);
+        slicefile << std::setw(w) << std::pow(vars_bin[isv[i]+((*it)+1)*nbins] / arad, 0.25);
 
         slicefile << std::endl;
     }

Diagnostics/Radiation/rad_source.cpp

@@ -81,7 +81,7 @@ int main(int argc, char* argv[])
 
         Real rhoe, rad;
 
-        fradsource(ARLIM_3D(bx.loVect()), ARLIM_3D(bx.hiVect()),
+        fradsource(AMREX_ARLIM_3D(bx.loVect()), AMREX_ARLIM_3D(bx.hiVect()),
                    BL_TO_FORTRAN_FAB(lev_data_mf[mfi]),
                    &rhoe, &rad, rhoe_comp, rad_comp);
 

Diagnostics/Radiation/rad_sphere.cpp

@@ -142,7 +142,7 @@ int main(int argc, char* argv[])
     // over levels, we will compare to the finest level index space to
     // determine if we've already output here
     int mask_size = domain.length()[0];
-    Vector<int> imask(pow(mask_size, AMREX_SPACEDIM), 1);
+    Vector<int> imask(std::pow(mask_size, AMREX_SPACEDIM), 1);
 
     // counter
     int cnt = 0;
@@ -163,12 +163,12 @@ int main(int argc, char* argv[])
         for (MFIter mfi(lev_data_mf, true); mfi.isValid(); ++mfi) {
             const Box& bx = mfi.tilebox();
 
-            fradsphere(ARLIM_3D(bx.loVect()), ARLIM_3D(bx.hiVect()),
-                       ZFILL(problo), ZFILL(probhi),
+            fradsphere(AMREX_ARLIM_3D(bx.loVect()), AMREX_ARLIM_3D(bx.hiVect()),
+                       AMREX_ZFILL(problo), AMREX_ZFILL(probhi),
                        BL_TO_FORTRAN_FAB(lev_data_mf[mfi]),
                        nbins, vars_bin.dataPtr(),
                        imask.dataPtr(), mask_size, r1,
-                       ZFILL(dx), &cnt);
+                       AMREX_ZFILL(dx), &cnt);
         }
 
         // adjust r1 for the next lowest level

Diagnostics/Radiation/rhd_shocktube.cpp

@@ -150,7 +150,7 @@ int main(int argc, char* argv[])
     for (MFIter mfi(lev_data_mf, true); mfi.isValid(); ++mfi) {
         const Box& bx = mfi.tilebox();
 
-        frhdshocktube(ARLIM_3D(bx.loVect()), ARLIM_3D(bx.hiVect()),
+        frhdshocktube(AMREX_ARLIM_3D(bx.loVect()), AMREX_ARLIM_3D(bx.hiVect()),
                       BL_TO_FORTRAN_FAB(lev_data_mf[mfi]),
                       nbins, dens_bin.dataPtr(), vel_bin.dataPtr(),
                       pres_bin.dataPtr(), rad_bin.dataPtr(),

Diagnostics/Sedov/main.cpp

@@ -148,7 +148,7 @@ int main(int argc, char* argv[])
 
 #else
     double x_maxdist = amrex::max(std::abs(probhi[0] - xctr),
-                                  std::fabs(problo[0] - xctr));
+                                  std::abs(problo[0] - xctr));
     double y_maxdist = amrex::max(std::abs(probhi[1] - yctr),
                                   std::abs(problo[1] - yctr));
     double z_maxdist = amrex::max(std::abs(probhi[2] - zctr),
@@ -342,10 +342,10 @@ int main(int argc, char* argv[])
     // write the data in columns
     const auto SMALL = 1.e-20;
     for (auto i = 0; i < nbins; i++) {
-        if (fabs(dens_bin[i]) < SMALL) dens_bin[i] = 0.0;
-        if (fabs( vel_bin[i]) < SMALL) vel_bin[i] = 0.0;
-        if (fabs(pres_bin[i]) < SMALL) pres_bin[i] = 0.0;
-        if (fabs(   e_bin[i]) < SMALL) e_bin[i] = 0.0;
+        if (std::abs(dens_bin[i]) < SMALL) dens_bin[i] = 0.0;
+        if (std::abs( vel_bin[i]) < SMALL) vel_bin[i] = 0.0;
+        if (std::abs(pres_bin[i]) < SMALL) pres_bin[i] = 0.0;
+        if (std::abs(   e_bin[i]) < SMALL) e_bin[i] = 0.0;
 
         slicefile << std::setw(w) << r[i] << std::setw(w) << dens_bin[i] << std::setw(w) << vel_bin[i] << std::setw(w) << pres_bin[i] << std::setw(w) << e_bin[i] << std::endl;
     }

Docs/rp.py

@@ -7,17 +7,17 @@
 from more_itertools import unique_everseen
 
 MAIN_HEADER = """
-+--------------------------------------------+-------------------------------------------------------------+---------------+
-| parameter                                  | description                                                 | default value |
-+============================================+=============================================================+===============+
++--------------------------------------------+-------------------------------------------------------------+-----------------------------+
+| parameter                                  | description                                                 | default value               |
++============================================+=============================================================+=============================+
 """
 
 SEPARATOR = """
-+--------------------------------------------+-------------------------------------------------------------+---------------+
++--------------------------------------------+-------------------------------------------------------------+-----------------------------+
 """
 
 ENTRY = """
-| {:42} | {:59} | {:13} |
+| {:42} | {:59} | {:27} |
 """
 
 WRAP_LEN = 59