AMReX/pyAMReX/PICSAR: weekly update (#5391)

- Weekly update to latest AMReX: ```console ./Tools/Release/updateAMReX.py ``` - Weekly update to latest pyAMReX: ```console ./Tools/Release/updatepyAMReX.py ``` - Weekly update to latest PICSAR (no changes): ```console ./Tools/Release/updatePICSAR.py ```
ECP-WarpX · Oct 21, 2024 · 05e09b1 · 05e09b1
1 parent 1c676b9
commit 05e09b1
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diff --git a/.github/workflows/cuda.yml b/.github/workflows/cuda.yml
@@ -137,7 +137,7 @@ jobs:
         which nvcc || echo "nvcc not in PATH!"
 
         git clone https://github.com/AMReX-Codes/amrex.git ../amrex
-        cd ../amrex && git checkout --detach e1222803739ed2342b9ff6fc2d57316ff0d6cb0c && cd -
+        cd ../amrex && git checkout --detach 62c2a81eac7862d526e5861ef2befc00b7f5b759 && cd -
         make COMP=gcc QED=FALSE USE_MPI=TRUE USE_GPU=TRUE USE_OMP=FALSE USE_FFT=TRUE USE_CCACHE=TRUE -j 4
 
         ccache -s

diff --git a/Docs/source/developers/particles.rst b/Docs/source/developers/particles.rst
@@ -141,7 +141,7 @@ Attribute name        ``int``/``real``  Description                         Wher
                                         Wheeler process                                physics is used.
 ====================  ================  ==================================  ===== ==== ======================
 
-WarpX allows extra runtime attributes to be added to particle containers (through ``AddRealComp("attrname")`` or ``AddIntComp("attrname")``).
+WarpX allows extra runtime attributes to be added to particle containers (through ``NewRealComp("attrname")`` or ``NewIntComp("attrname")``).
 The attribute name can then be used to access the values of that attribute.
 For example, using a particle iterator, ``pti``, to loop over the particles the command ``pti.GetAttribs(particle_comps["attrname"]).dataPtr();`` will return the values of the ``"attrname"`` attribute.
 

diff --git a/Source/Diagnostics/ParticleIO.cpp b/Source/Diagnostics/ParticleIO.cpp
@@ -173,7 +173,7 @@ MultiParticleContainer::Restart (const std::string& dir)
                     + " was found in the checkpoint file, but it has not been added yet. "
                     + " Adding it now."
                 );
-                pc->AddRealComp(comp_name);
+                pc->NewRealComp(comp_name);
             }
         }
 
@@ -206,7 +206,7 @@ MultiParticleContainer::Restart (const std::string& dir)
                     + " was found in the checkpoint file, but it has not been added yet. "
                     + " Adding it now."
                 );
-                pc->AddIntComp(comp_name);
+                pc->NewIntComp(comp_name);
             }
         }
 
@@ -258,7 +258,7 @@ storePhiOnParticles ( PinnedMemoryParticleContainer& tmp,
         is_full_diagnostic,
         "Output of the electrostatic potential (phi) on the particles was requested, "
         "but this is only available with `diag_type = Full`.");
-    tmp.AddRealComp("phi");
+    tmp.NewRealComp("phi");
     int const phi_index = tmp.getParticleComps().at("phi");
     auto& warpx = WarpX::GetInstance();
 #ifdef AMREX_USE_OMP

diff --git a/Source/Initialization/WarpXInitData.cpp b/Source/Initialization/WarpXInitData.cpp
@@ -688,15 +688,15 @@ WarpX::InitFromScratch ()
         // Add space to save the positions and velocities at the start of the time steps
         for (auto const& pc : *mypc) {
 #if (AMREX_SPACEDIM >= 2)
-            pc->AddRealComp("x_n");
+            pc->NewRealComp("x_n");
 #endif
 #if defined(WARPX_DIM_3D) || defined(WARPX_DIM_RZ)
-            pc->AddRealComp("y_n");
+            pc->NewRealComp("y_n");
 #endif
-            pc->AddRealComp("z_n");
-            pc->AddRealComp("ux_n");
-            pc->AddRealComp("uy_n");
-            pc->AddRealComp("uz_n");
+            pc->NewRealComp("z_n");
+            pc->NewRealComp("ux_n");
+            pc->NewRealComp("uy_n");
+            pc->NewRealComp("uz_n");
         }
 
     }

diff --git a/Source/Particles/NamedComponentParticleContainer.H b/Source/Particles/NamedComponentParticleContainer.H
@@ -159,7 +159,7 @@ public:
      * @param name Name of the new component
      * @param comm Whether to communicate this component, in the particle Redistribute
      */
-    void AddRealComp (const std::string& name, bool comm=true)
+    void NewRealComp (const std::string& name, bool comm=true)
     {
         auto search = particle_comps.find(name);
         if (search == particle_comps.end()) {
@@ -177,7 +177,7 @@ public:
      * @param name Name of the new component
      * @param comm Whether to communicate this component, in the particle Redistribute
      */
-    void AddIntComp (const std::string& name, bool comm=true)
+    void NewIntComp (const std::string& name, bool comm=true)
     {
         auto search = particle_icomps.find(name);
         if (search == particle_icomps.end()) {

diff --git a/Source/Particles/ParticleBoundaryBuffer.cpp b/Source/Particles/ParticleBoundaryBuffer.cpp
@@ -384,11 +384,11 @@ void ParticleBoundaryBuffer::gatherParticlesFromDomainBoundaries (MultiParticleC
                 if (!buffer[i].isDefined())
                 {
                     buffer[i] = pc.make_alike<amrex::PinnedArenaAllocator>();
-                    buffer[i].AddIntComp("stepScraped", false);
-                    buffer[i].AddRealComp("deltaTimeScraped", false);
-                    buffer[i].AddRealComp("nx", false);
-                    buffer[i].AddRealComp("ny", false);
-                    buffer[i].AddRealComp("nz", false);
+                    buffer[i].NewIntComp("stepScraped", false);
+                    buffer[i].NewRealComp("deltaTimeScraped", false);
+                    buffer[i].NewRealComp("nx", false);
+                    buffer[i].NewRealComp("ny", false);
+                    buffer[i].NewRealComp("nz", false);
                 }
 
                 auto& species_buffer = buffer[i];
@@ -481,11 +481,11 @@ void ParticleBoundaryBuffer::gatherParticlesFromEmbeddedBoundaries (
             if (!buffer[i].isDefined())
             {
                 buffer[i] = pc.make_alike<amrex::PinnedArenaAllocator>();
-                buffer[i].AddIntComp("stepScraped", false);
-                buffer[i].AddRealComp("deltaTimeScraped", false);
-                buffer[i].AddRealComp("nx", false);
-                buffer[i].AddRealComp("ny", false);
-                buffer[i].AddRealComp("nz", false);
+                buffer[i].NewIntComp("stepScraped", false);
+                buffer[i].NewRealComp("deltaTimeScraped", false);
+                buffer[i].NewRealComp("nx", false);
+                buffer[i].NewRealComp("ny", false);
+                buffer[i].NewRealComp("nz", false);
 
             }
 

diff --git a/Source/Particles/PhysicalParticleContainer.cpp b/Source/Particles/PhysicalParticleContainer.cpp
@@ -342,12 +342,12 @@ PhysicalParticleContainer::PhysicalParticleContainer (AmrCore* amr_core, int isp
 #ifdef WARPX_QED
     pp_species_name.query("do_qed_quantum_sync", m_do_qed_quantum_sync);
     if (m_do_qed_quantum_sync) {
-        AddRealComp("opticalDepthQSR");
+        NewRealComp("opticalDepthQSR");
     }
 
     pp_species_name.query("do_qed_breit_wheeler", m_do_qed_breit_wheeler);
     if (m_do_qed_breit_wheeler) {
-        AddRealComp("opticalDepthBW");
+        NewRealComp("opticalDepthBW");
     }
 
     if(m_do_qed_quantum_sync){
@@ -368,7 +368,7 @@ PhysicalParticleContainer::PhysicalParticleContainer (AmrCore* amr_core, int isp
             str_int_attrib_function.at(i));
         m_user_int_attrib_parser.at(i) = std::make_unique<amrex::Parser>(
             utils::parser::makeParser(str_int_attrib_function.at(i),{"x","y","z","ux","uy","uz","t"}));
-        AddIntComp(m_user_int_attribs.at(i));
+        NewIntComp(m_user_int_attribs.at(i));
     }
 
     // User-defined real attributes
@@ -383,19 +383,19 @@ PhysicalParticleContainer::PhysicalParticleContainer (AmrCore* amr_core, int isp
             str_real_attrib_function.at(i));
         m_user_real_attrib_parser.at(i) = std::make_unique<amrex::Parser>(
             utils::parser::makeParser(str_real_attrib_function.at(i),{"x","y","z","ux","uy","uz","t"}));
-        AddRealComp(m_user_real_attribs.at(i));
+        NewRealComp(m_user_real_attribs.at(i));
     }
 
     // If old particle positions should be saved add the needed components
     pp_species_name.query("save_previous_position", m_save_previous_position);
     if (m_save_previous_position) {
 #if (AMREX_SPACEDIM >= 2)
-        AddRealComp("prev_x");
+        NewRealComp("prev_x");
 #endif
 #if defined(WARPX_DIM_3D)
-        AddRealComp("prev_y");
+        NewRealComp("prev_y");
 #endif
-        AddRealComp("prev_z");
+        NewRealComp("prev_z");
 #ifdef WARPX_DIM_RZ
       amrex::Abort("Saving previous particle positions not yet implemented in RZ");
 #endif
@@ -3121,7 +3121,7 @@ PhysicalParticleContainer::InitIonizationModule ()
         physical_element == "H" || !do_adk_correction,
         "Correction to ADK by Zhang et al., PRA 90, 043410 (2014) only works with Hydrogen");
     // Add runtime integer component for ionization level
-    AddIntComp("ionizationLevel");
+    NewIntComp("ionizationLevel");
     // Get atomic number and ionization energies from file
     const int ion_element_id = utils::physics::ion_map_ids.at(physical_element);
     ion_atomic_number = utils::physics::ion_atomic_numbers[ion_element_id];

diff --git a/Source/Python/Particles/WarpXParticleContainer.cpp b/Source/Python/Particles/WarpXParticleContainer.cpp
@@ -30,7 +30,7 @@ void init_WarpXParticleContainer (py::module& m)
     > wpc (m, "WarpXParticleContainer");
     wpc
         .def("add_real_comp",
-            [](WarpXParticleContainer& pc, const std::string& name, bool comm) { pc.AddRealComp(name, comm); },
+            [](WarpXParticleContainer& pc, const std::string& name, bool comm) { pc.NewRealComp(name, comm); },
             py::arg("name"), py::arg("comm")
         )
         .def("add_n_particles",

diff --git a/cmake/dependencies/AMReX.cmake b/cmake/dependencies/AMReX.cmake
@@ -283,7 +283,7 @@ set(WarpX_amrex_src ""
 set(WarpX_amrex_repo "https://github.com/AMReX-Codes/amrex.git"
     CACHE STRING
     "Repository URI to pull and build AMReX from if(WarpX_amrex_internal)")
-set(WarpX_amrex_branch "e1222803739ed2342b9ff6fc2d57316ff0d6cb0c"
+set(WarpX_amrex_branch "62c2a81eac7862d526e5861ef2befc00b7f5b759"
     CACHE STRING
     "Repository branch for WarpX_amrex_repo if(WarpX_amrex_internal)")
 

diff --git a/cmake/dependencies/pyAMReX.cmake b/cmake/dependencies/pyAMReX.cmake
@@ -74,7 +74,7 @@ option(WarpX_pyamrex_internal "Download & build pyAMReX" ON)
 set(WarpX_pyamrex_repo "https://github.com/AMReX-Codes/pyamrex.git"
     CACHE STRING
     "Repository URI to pull and build pyamrex from if(WarpX_pyamrex_internal)")
-set(WarpX_pyamrex_branch "3699781e4284921f9ccdbbbbc57169ff79c0de20"
+set(WarpX_pyamrex_branch "d96b4948cc5812be82dbff1df5d62927c866ae07"
     CACHE STRING
     "Repository branch for WarpX_pyamrex_repo if(WarpX_pyamrex_internal)")