Merge branch 'development' of https://github.com/AMReX-Codes/amrex into test-set_eb_data

Author: eebasso

.clang-tidy

@@ -53,7 +53,6 @@ Checks: >
      readability-*,
        -readability-avoid-nested-conditional-operator,
        -readability-avoid-unconditional-preprocessor-if,
-       -readability-container-contains,
        -readability-else-after-return,
        -readability-function-cognitive-complexity,
        -readability-function-size,
@@ -85,4 +84,3 @@ HeaderFileExtensions: ['', "H", 'h', 'hh', 'hpp', 'hxx']
 # -modernize-use-ranges
 # -modernize-use-integer-sign-comparison
 # -modernize-use-starts-ends-with
-# -readability-container-contains

Docs/sphinx_documentation/source/LinearSolvers.rst

@@ -863,14 +863,16 @@ discretized form of
 
 .. math:: \nabla \times (\alpha \nabla \times \vec{E}) + \beta \vec{E} = \vec{f},
 
-where :math:`\vec{E}` and :math:`\vec{f}` are defined on cell edges,
-:math:`\alpha` is a positive scalar, and :math:`\beta` is a non-negative
-scalar (either a constant or a field). An :cpp:`Array` of three
-:cpp:`MultiFab`\ s is used to store the components of :math:`\vec{E}` and
-:math:`\vec{f}`. It is the user's responsibility to ensure that the
-right-hand-side data are consistent on edges shared by multiple
-:cpp:`Box`\ es.  If needed, you can call :cpp:`MLCurlCurl::prepareRHS` to
-perform this synchronization.
+where :math:`\vec{E}` and :math:`\vec{f}` are defined on cell edges.  The
+coefficient :math:`\alpha` may be supplied either as a single positive
+scalar through :cpp:`MLCurlCurl::setScalars`, or as a nodal :cpp:`MultiFab`
+by calling :cpp:`MLCurlCurl::setAlpha` with one entry per AMR level. The
+:math:`\beta` term can be a non-negative scalar or an edge-centered field
+set via :cpp:`setBeta`. An :cpp:`Array` of three :cpp:`MultiFab`\ s is used
+to store the components of :math:`\vec{E}` and :math:`\vec{f}`. It is the
+user's responsibility to ensure that the right-hand-side data are consistent
+on edges shared by multiple :cpp:`Box`\ es.  If needed, you can call
+:cpp:`MLCurlCurl::prepareRHS` to perform this synchronization.
 
 The solver supports 1D, 2D and 3D. Note that even in the 1D and 2D cases,
 :math:`\vec{E}` still has three components, one for each spatial

Src/Base/AMReX_CArena.cpp

@@ -121,7 +121,7 @@ CArena::alloc_protected (std::size_t nbytes)
     else
     {
         BL_ASSERT((*free_it).size() >= nbytes);
-        BL_ASSERT(m_busylist.find(*free_it) == m_busylist.end());
+        BL_ASSERT(!m_busylist.contains(*free_it));
 
         vp = (*free_it).block();
 
@@ -174,7 +174,7 @@ CArena::alloc_in_place (void* pt, std::size_t szmin, std::size_t szmax)
             amrex::Abort("CArena::alloc_in_place: unknown pointer");
             return std::make_pair(nullptr,0);
         }
-        AMREX_ASSERT(m_freelist.find(*busy_it) == m_freelist.end());
+        AMREX_ASSERT(!m_freelist.contains(*busy_it));
 
         if (busy_it->size() >= szmax) {
             return std::make_pair(pt, busy_it->size());
@@ -248,7 +248,7 @@ CArena::shrink_in_place (void* pt, std::size_t new_size)
         amrex::Abort("CArena::shrink_in_place: unknown pointer");
         return nullptr;
     }
-    AMREX_ASSERT(m_freelist.find(*busy_it) == m_freelist.end());
+    AMREX_ASSERT(!m_freelist.contains(*busy_it));
 
     auto const old_size = busy_it->size();
 
@@ -312,7 +312,7 @@ CArena::free (void* vp)
         amrex::Abort("CArena::free: unknown pointer");
         return;
     }
-    BL_ASSERT(m_freelist.find(*busy_it) == m_freelist.end());
+    BL_ASSERT(!m_freelist.contains(*busy_it));
 
     m_actually_used -= busy_it->size();
 

Src/Base/AMReX_FACopyDescriptor.H

@@ -475,7 +475,7 @@ FabArrayCopyDescriptor<FAB>::CollectData ()
 
         Total_Rcvs_Size += Cnt;
 
-        if (Rcvs.count(Who) > 0)
+        if (Rcvs.contains(Who))
         {
             Rcvs[Who] += 1;
         }
@@ -484,7 +484,7 @@ FabArrayCopyDescriptor<FAB>::CollectData ()
             Rcvs[Who] = 1;
         }
 
-        if (Npts.count(Who) > 0)
+        if (Npts.contains(Who))
         {
             Npts[Who] += Cnt;
         }
@@ -493,7 +493,7 @@ FabArrayCopyDescriptor<FAB>::CollectData ()
             Npts[Who] = Cnt;
         }
     }
-    BL_ASSERT(Rcvs.count(MyProc) == 0);
+    BL_ASSERT(!Rcvs.contains(MyProc));
 
     BL_ASSERT((Total_Rcvs_Size*sizeof(value_type))
               < static_cast<std::size_t>(std::numeric_limits<int>::max()));

Src/Base/AMReX_ForkJoin.H

@@ -106,7 +106,7 @@ class ForkJoin
     // TODO: may want to de-register MFs if they change across invocations
 
     MultiFab &get_mf (const std::string &name, int idx = 0) {
-        AMREX_ASSERT_WITH_MESSAGE(data.count(name) > 0 && idx < data[name].size(), "get_mf(): name or index not found");
+        AMREX_ASSERT_WITH_MESSAGE(data.contains(name) && idx < data[name].size(), "get_mf(): name or index not found");
         AMREX_ASSERT(task_me >= 0 && task_me < data[name][idx].forked.size());
         return data[name][idx].forked[task_me];
     }

Src/Base/AMReX_ForkJoin.cpp

@@ -140,7 +140,7 @@ ForkJoin::reg_mf (MultiFab &mf, const std::string &name, int idx,
 void
 ForkJoin::modify_ngrow (const std::string &name, int idx, IntVect ngrow)
 {
-    AMREX_ALWAYS_ASSERT_WITH_MESSAGE(data.count(name) > 0 && data[name].size() > idx,
+    AMREX_ALWAYS_ASSERT_WITH_MESSAGE(data.contains(name) && data[name].size() > idx,
                                      "(name, index) pair doesn't exist");
     AMREX_ALWAYS_ASSERT_WITH_MESSAGE(!flag_invoked,
                                      "Can only specify grow cells before first forkjoin() invocation");
@@ -154,7 +154,7 @@ ForkJoin::modify_ngrow (const std::string &name, int idx, IntVect ngrow)
 void
 ForkJoin::modify_split (const std::string &name, int idx, Vector<ComponentSet> comp_split)
 {
-    AMREX_ALWAYS_ASSERT_WITH_MESSAGE(data.count(name) > 0 && data[name].size() > idx,
+    AMREX_ALWAYS_ASSERT_WITH_MESSAGE(data.contains(name) && data[name].size() > idx,
                                      "(name, index) pair doesn't exist");
     AMREX_ALWAYS_ASSERT_WITH_MESSAGE(!flag_invoked,
                                      "Can only specify custom split before first forkjoin() invocation");

Src/Base/AMReX_GpuAtomic.H

@@ -18,8 +18,7 @@ namespace Gpu::Atomic {
 // For LogicalOr and LogicalAnd, the data type is int.
 // For Exch and CAS, the data type is generic.
 // All these functions are non-atomic in host code!!!
-// If one needs them to be atomic in host code, use HostDevice::Atomic::*.  Currently only
-// HostDevice::Atomic::Add is supported.  We could certainly add more.
+// If one needs them to be atomic in host code, use HostDevice::Atomic::*.
 // If we add more types for atomicAdd, we also need to update HasAtomicAdd in AMReX_TypeTraits.H.
 
 /// \cond DOXYGEN_IGNORE
@@ -617,6 +616,21 @@ namespace HostDevice::Atomic {
         *sum += value;
     }
 
+    template <class T>
+    AMREX_FORCE_INLINE
+    T FetchAdd_Host (T* const sum, T const value) noexcept
+    {
+        T old;
+#ifdef AMREX_USE_OMP
+#pragma omp atomic capture
+#endif
+        {
+            old = *sum;
+            *sum += value;
+        }
+        return old;
+    }
+
     template <class T>
     AMREX_GPU_HOST_DEVICE AMREX_FORCE_INLINE
     void Add (T* const sum, T const value) noexcept
@@ -625,6 +639,14 @@ namespace HostDevice::Atomic {
         AMREX_IF_ON_HOST((Add_Host(sum,value);))
     }
 
+    template <class T>
+    AMREX_GPU_HOST_DEVICE AMREX_FORCE_INLINE
+    T FetchAdd (T* const sum, T const value) noexcept
+    {
+        AMREX_IF_ON_DEVICE((return Gpu::Atomic::Add(sum,value);))
+        AMREX_IF_ON_HOST((return FetchAdd_Host(sum,value);))
+    }
+
 }
 
 #ifdef AMREX_USE_GPU

Src/Base/AMReX_Random.cpp

@@ -208,7 +208,7 @@ UniqueRandomSubset (Vector<int> &uSet, int setSize, int poolSize,
   uSet.clear();
   while(static_cast<int>(copySet.size()) < setSize) {
     int r = static_cast<int>(Random_int(poolSize));
-    if(copySet.find(r) == copySet.end()) {
+    if(!copySet.contains(r)) {
       copySet.insert(r);
       uSet.push_back(r);
     }

Src/Base/AMReX_TinyProfiler.cpp

@@ -421,7 +421,7 @@ TinyProfiler::Finalize (bool bFlushing)
 
         if (!alreadySynced) {
             for (auto const& s : syncedRegions) {
-                if (lstatsmap.find(s) == lstatsmap.end()) {
+                if (!lstatsmap.contains(s)) {
                     lstatsmap.insert(std::make_pair(s,std::map<std::string,Stats>()));
                 }
             }
@@ -529,7 +529,7 @@ TinyProfiler::PrintStats (std::map<std::string,Stats>& regstats, double dt_max,
 
         if (! alreadySynced) {  // add the new name
             for (auto const& s : syncedStrings) {
-                if (regstats.find(s) == regstats.end()) {
+                if (!regstats.contains(s)) {
                     regstats.insert(std::make_pair(s, Stats()));
                 }
             }
@@ -744,7 +744,7 @@ TinyProfiler::PrintMemStats (std::map<std::string, MemStat>& memstats,
 
         if (! alreadySynced) {  // add the new name
             for (auto const& s : syncedStrings) {
-                if (memstats.find(s) == memstats.end()) {
+                if (!memstats.contains(s)) {
                     memstats[s]; // insert
                 }
             }

Src/Base/AMReX_VisMF.H

@@ -668,7 +668,7 @@ Read (FabArray<FAB>& fa, const std::string& name)
                 auto whichread = allreads[fi].begin();
                 for ( ; whichread != allreads[fi].end(); ++whichread) {
                     const int tryproc = whichread->first;
-                    if (busyprocs.find(tryproc) == busyprocs.end()) { // not busy
+                    if (!busyprocs.contains(tryproc)) { // not busy
                         busyprocs.insert(tryproc);
                         Vector<int> vreads;
                         vreads.reserve(whichread->second.size());