[WIP] AMReX/pyAMReX/PICSAR: weekly update

.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

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.
 

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

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");
  }
 
  }

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()) {

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);
 
  }
 

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];

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",

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)")
 

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 "fdd9c8cc8f9092ddbd5f29275393cf1329d7ac14"
  CACHE STRING
  "Repository branch for WarpX_pyamrex_repo if(WarpX_pyamrex_internal)")