Merge branch 'development' of https://github.com/AMReX-Codes/amrex in…

…to comments-linop-AB-convention

.github/workflows/cleanup-cache-postpr.yml

@@ -31,7 +31,10 @@ jobs:
           set +e
 
           keys=$(gh actions-cache list -L 100 -R $REPO -B $BRANCH | cut -f 1)
+          # $keys might contain spaces. Thus we set IFS to \n.
+          IFS=$'\n'
           for k in $keys
           do
-            gh actions-cache delete $k -R $REPO -B $BRANCH --confirm
+            gh actions-cache delete "$k" -R $REPO -B $BRANCH --confirm
           done
+          unset IFS

.github/workflows/cleanup-cache.yml

@@ -27,7 +27,7 @@ jobs:
           EVENT=${{ github.event.workflow_run.event }}
 
           # Triggering workflow run name (e.g., LinuxClang)
-          WORKFLOW_NAME=${{ github.event.workflow_run.name }}
+          WORKFLOW_NAME="${{ github.event.workflow_run.name }}"
 
           if [[ $EVENT == "pull_request" ]]; then
             gh run download ${{ github.event.workflow_run.id }} -n pr_number
@@ -45,16 +45,19 @@ jobs:
           # The goal is to keep the last used key of each job and delete all others.
 
           # something like ccache-LinuxClang-
-          keyprefix=ccache-${WORKFLOW_NAME}-
+          keyprefix="ccache-${WORKFLOW_NAME}-"
 
-          cached_jobs=$(gh actions-cache list -L 100 -R $REPO -B $BRANCH --key $keyprefix | awk -F '-git-' '{print $1}' | sort | uniq)
+          cached_jobs=$(gh actions-cache list -L 100 -R $REPO -B $BRANCH --key "$keyprefix" | awk -F '-git-' '{print $1}' | sort | uniq)
 
           # cached_jobs is something like "ccache-LinuxClang-configure-1d ccache-LinuxClang-configure-2d".
+          # It might also contain spaces. Thus we set IFS to \n.
+          IFS=$'\n'
           for j in $cached_jobs
           do
-            old_keys=$(gh actions-cache list -L 100 -R $REPO -B $BRANCH --key ${j}-git- --sort last-used | cut -f 1 | tail -n +2)
+            old_keys=$(gh actions-cache list -L 100 -R $REPO -B $BRANCH --key "${j}-git-" --sort last-used | cut -f 1 | tail -n +2)
             for k in $old_keys
             do
-              gh actions-cache delete $k -R $REPO -B $BRANCH --confirm
+              gh actions-cache delete "$k" -R $REPO -B $BRANCH --confirm
             done
           done
+          unset IFS

.github/workflows/codeql.yml

@@ -14,6 +14,7 @@ concurrency:
 
 jobs:
   analyze:
+    if: ${{ github.repository == 'AMReX-Codes/amrex' || github.event_name != 'schedule' }}
     name: Analyze
     runs-on: ubuntu-latest
     permissions:

CHANGES

@@ -1,3 +1,44 @@
+# 23.12
+
+  -- solve_cg: avoid use of MF `z` (#3637)
+
+  -- Fix: nosmt OMP Threads Default (#3647)
+     `amrex.omp_threads`: Can Avoid SMT (#3607)
+
+  -- When checking for periodic outs on GPU, copy full particle data (#3646)
+
+  -- MLEBABecLap: Support Robin BC at Domain Boundaries (#3617)
+
+  -- Ascent: SoA Particle Support (#3350)
+
+  -- solve_bicgstab: use fewer MFs (#3635)
+
+  -- solve_bicgstab: cut use of `s` (#3629)
+
+  -- Bug fix for amrex::Subtract when called with interger nghost (#3634)
+
+  -- Fix typo in `MLMGT<MF>::getGradSolution` when `MF` is different from `AMF` (#3631)
+
+  -- SUNDIALS: Use sunrealtype instead of realtype (#3632)
+
+  -- SYCL: Use get_multi_ptr instead of get_pointer (#3630)
+
+  -- Plotfile Tools: GPU support (#3626)
+
+  -- solve_cg: use linop.make instead of MF constructor (#3627)
+
+  -- CArena: shrink_in_place and operator<< (#3621)
+
+  -- solve_bicgstab: use linop.make instead of MF constructor (#3619)
+
+  -- replace AMREX_DEVICE_COMPILE with AMREX_IF_ON_DEVICE and AMREX_IF_ON_HOST (#3591)
+
+  -- [Breaking] Prefix `amrex_` to each plotfile Tool (#3600)
+
+  -- FillRandom: Use MKL host API (#3536)
+
+  -- use hipPointerAttribute_t.type as HIP is removing hipPointerAttribute_t.memoryType (#3610)
+
 # 23.11
 
   -- Give FlashFluxRegisters ways to accumulate data in registers (#3597)

Docs/sphinx_documentation/source/LinearSolvers.rst

@@ -483,7 +483,9 @@ To set homogeneous Dirichlet boundary conditions, call
     ml_ebabeclap->setEBHomogDirichlet(lev, coeff);
 
 where coeff can be a real number (i.e. the value is the same at every cell)
-or is the MultiFab holding the coefficient of the gradient at each cell with an EB face.
+or a MultiFab holding the coefficient of the gradient at each cell with an EB face.
+In other words, coeff is :math:`\beta` in the canonical form given in equation :eq:`eqn::abeclap`
+located at the EB surface centroid.
 
 To set inhomogeneous Dirichlet boundary conditions, call
 
@@ -494,8 +496,9 @@ To set inhomogeneous Dirichlet boundary conditions, call
     ml_ebabeclap->setEBDirichlet(lev, phi_on_eb, coeff);
 
 where phi_on_eb is the MultiFab holding the Dirichlet values in every cut cell,
-and coeff again is a real number (i.e. the value is the same at every cell)
-or a MultiFab holding the coefficient of the gradient at each cell with an EB face.
+and coeff again is a real number
+or a MultiFab holding the coefficient of the gradient at each cell with an EB face,
+i.e. :math:`\beta` in equation :eq:`eqn::abeclap` located at the EB surface centroid.
 
 Currently there are options to define the face-based coefficients on
 face centers vs face centroids, and to interpret the solution variable

Docs/sphinx_documentation/source/conf.py

@@ -42,7 +42,7 @@ def get_amrex_version():
 
 intersphinx_mapping = {
     'amrex_tutorials': ('https://amrex-codes.github.io/amrex/tutorials_html/', None),
-    'amrex_hydro':('https://amrex-codes.github.io/amrex/hydro_html/', None)
+    'amrex_hydro':('https://amrex-fluids.github.io/amrex-hydro/docs_html/', None)
 }
 
 # Add any paths that contain templates here, relative to this directory.

Src/AmrCore/AMReX_AmrMesh.cpp

@@ -1082,7 +1082,7 @@ AmrMesh::checkInput ()
     for (int i = 0; i < max_level; i++)
     {
         if (MaxRefRatio(i) < 2) {
-            amrex::Error("Amr::checkInput: bad ref_ratios");
+            amrex::Warning("Amr::checkInput: ref_ratios all equal to one!");
         }
     }
 

Src/Base/AMReX_BaseFab.H

@@ -90,54 +90,6 @@ makeArray4 (T* p, Box const& bx, int ncomp) noexcept
     return Array4<T>{p, amrex::begin(bx), amrex::end(bx), ncomp};
 }
 
-/**
-*  \brief A Fortran Array-like Object
-*  BaseFab emulates the Fortran array concept.
-*  Useful operations can be performed upon
-*  BaseFabs in C++, and they provide a convenient interface to
-*  Fortran when it is necessary to retreat into that language.
-
-*  BaseFab is a template class.  Through use of the
-*  template, a BaseFab may be based upon any class.  So far at least,
-*  most applications have been based upon simple types like integers,
-*  real*4s, or real*8s.  Most applications do not use BaseFabs
-*  directly, but utilize specialized classes derived from BaseFab.
-
-*  Classes derived from BaseFab include FArrayBox, IArrayBox, TagBox,
-*  Mask, EBFArrayBox, EBCellFlag and CutFab.
-
-*  BaseFab objects depend on the dimensionality of space
-*  (indirectly through the DOMAIN Box member).  It is
-*  typical to define the macro SPACEDIM to be 1, 2, or 3 to indicate
-*  the dimension of space.  See the discussion of class Box for more
-*  information.  A BaseFab contains a Box DOMAIN, which indicates the
-*  integer indexing space over which the array is defined.  A BaseFab
-*  also has NVAR components.  By components, we mean that for each
-*  point in the rectangular indexing space, there are NVAR values
-*  associated with that point.  A Fortran array corresponding to a
-*  BaseFab would have (SPACEDIM+1) dimensions.
-
-*  By design, the array layout in a BaseFab mirrors that of a
-*  Fortran array.  The first index (x direction for example) varies
-*  most rapidly, the next index (y direction), if any, varies next
-*  fastest. The component index varies last, after all the spatial
-*  indices.
-
-*  It is sometimes convenient to be able to treat a sub-array within an
-*  existing BaseFab as a BaseFab in its own right.  This is often
-*  referred to as aliasing the BaseFab.  Note that when aliasing is
-*  used, the BaseFabs domain will not, in general, be the same as the
-*  parent BaseFabs domain, nor will the number of components.
-*  BaseFab is a dimension dependent class, so SPACEDIM must be
-*  defined as either 1, 2, or 3 when compiling.
-
-*  This is NOT a polymorphic class.
-
-*  It does NOT provide a copy constructor or assignment operator.
-
-*  T MUST have a default constructor and an assignment operator.
-*/
-
 template <typename T>
 typename std::enable_if<std::is_arithmetic<T>::value>::type
 placementNew (T* const /*ptr*/, Long /*n*/)
@@ -178,6 +130,54 @@ placementDelete (T* const ptr, Long n)
     });
 }
 
+/**
+ * \brief A FortranArrayBox(FAB)-like object
+ *
+ * BaseFab emulates the Fortran array concept.
+ * Useful operations can be performed upon
+ * BaseFabs in C++, and they provide a convenient interface to
+ * Fortran when it is necessary to retreat into that language.
+ *
+ * BaseFab is a template class.  Through use of the
+ * template, a BaseFab may be based upon any class.  So far at least,
+ * most applications have been based upon simple types like integers,
+ * real*4s, or real*8s.  Most applications do not use BaseFabs
+ * directly, but utilize specialized classes derived from BaseFab.
+ *
+ * Classes derived from BaseFab include FArrayBox, IArrayBox, TagBox,
+ * Mask, EBFArrayBox, EBCellFlag and CutFab.
+ *
+ * BaseFab objects depend on the dimensionality of space
+ * (indirectly through the DOMAIN Box member).  It is
+ * typical to define the macro SPACEDIM to be 1, 2, or 3 to indicate
+ * the dimension of space.  See the discussion of class Box for more
+ * information.  A BaseFab contains a Box DOMAIN, which indicates the
+ * integer indexing space over which the array is defined.  A BaseFab
+ * also has NVAR components.  By components, we mean that for each
+ * point in the rectangular indexing space, there are NVAR values
+ * associated with that point.  A Fortran array corresponding to a
+ * BaseFab would have (SPACEDIM+1) dimensions.
+ *
+ * By design, the array layout in a BaseFab mirrors that of a
+ * Fortran array.  The first index (x direction for example) varies
+ * most rapidly, the next index (y direction), if any, varies next
+ * fastest. The component index varies last, after all the spatial
+ * indices.
+ *
+ * It is sometimes convenient to be able to treat a sub-array within an
+ * existing BaseFab as a BaseFab in its own right.  This is often
+ * referred to as aliasing the BaseFab.  Note that when aliasing is
+ * used, the BaseFabs domain will not, in general, be the same as the
+ * parent BaseFabs domain, nor will the number of components.
+ * BaseFab is a dimension dependent class, so SPACEDIM must be
+ * defined as either 1, 2, or 3 when compiling.
+ *
+ * This is NOT a polymorphic class.
+ *
+ * It does NOT provide a copy constructor or assignment operator.
+ *
+ * \tparam T MUST have a default constructor and an assignment operator.
+ */
 template <class T>
 class BaseFab
     : public DataAllocator

Src/Base/AMReX_BoxArray.H

@@ -515,16 +515,16 @@ struct BATransformer
 // for backward compatibility
 using BndryBATransformer = BATransformer;
 
-/**
-* \brief A collection of Boxes stored in an Array.  It is a
-* reference-counted concrete class, not a polymorphic one; i.e. you
-* cannot use any of the List member functions with a BoxList.
-*/
-
 class MFIter;
 class AmrMesh;
 class FabArrayBase;
 
+/**
+ * \brief A collection of Boxes stored in an Array.
+ *
+ * It is a reference-counted concrete class, not a polymorphic one; i.e. you
+ * cannot use any of the List member functions with a BoxList.
+ */
 class BoxArray
 {
 public:

Src/Base/AMReX_FArrayBox.H

@@ -26,7 +26,6 @@ class FArrayBox;
 * primarily for FArrayBox implementers; i.e. user's shouldn't
 * call any of the member functions in this class directly.
 */
-
 class FABio // NOLINT(cppcoreguidelines-special-member-functions)
 {
 public:
@@ -224,7 +223,6 @@ private:
 *  This class does NOT provide a copy constructor or assignment operator,
 *  but it has a move constructor.
 */
-
 class FArrayBox
     :
     public BaseFab<Real>