Merge remote-tracking branch 'upstream/development' into remove_calls…

…_to_warpx_get_instance_from_macroscopic_properties
lucafedeli88 · Apr 24, 2024 · cda66e8 · cda66e8
2 parents 61e69af + cbe4355
commit cda66e8
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diff --git a/.github/workflows/cuda.yml b/.github/workflows/cuda.yml
@@ -115,7 +115,7 @@ jobs:
         which nvcc || echo "nvcc not in PATH!"
 
         git clone https://github.com/AMReX-Codes/amrex.git ../amrex
-        cd ../amrex && git checkout --detach 7813bb7d6bc6cea658edac1f2bde046c7d174168 && cd -
+        cd ../amrex && git checkout --detach b752027c1aebdfb4be339b1e30932b4108286a7a && cd -
         make COMP=gcc QED=FALSE USE_MPI=TRUE USE_GPU=TRUE USE_OMP=FALSE USE_PSATD=TRUE USE_CCACHE=TRUE -j 4
 
         ccache -s

diff --git a/.github/workflows/macos.yml b/.github/workflows/macos.yml
@@ -36,9 +36,6 @@ jobs:
         brew tap openpmd/openpmd
         brew install openpmd-api
 
-        python3 -m pip install --upgrade pip
-        python3 -m pip install --upgrade virtualenv
-
         python3 -m venv py-venv
         source py-venv/bin/activate
         python3 -m pip install --upgrade pip

diff --git a/Regression/WarpX-GPU-tests.ini b/Regression/WarpX-GPU-tests.ini
@@ -60,7 +60,7 @@ emailBody = Check https://ccse.lbl.gov/pub/GpuRegressionTesting/WarpX/ for more
 
 [AMReX]
 dir = /home/regtester/git/amrex/
-branch = 7813bb7d6bc6cea658edac1f2bde046c7d174168
+branch = b752027c1aebdfb4be339b1e30932b4108286a7a
 
 [source]
 dir = /home/regtester/git/WarpX

diff --git a/Regression/WarpX-tests.ini b/Regression/WarpX-tests.ini
@@ -59,7 +59,7 @@ emailBody = Check https://ccse.lbl.gov/pub/RegressionTesting/WarpX/ for more det
 
 [AMReX]
 dir = /home/regtester/AMReX_RegTesting/amrex/
-branch = 7813bb7d6bc6cea658edac1f2bde046c7d174168
+branch = b752027c1aebdfb4be339b1e30932b4108286a7a
 
 [source]
 dir = /home/regtester/AMReX_RegTesting/warpx

diff --git a/Source/BoundaryConditions/PML_current.H b/Source/BoundaryConditions/PML_current.H
@@ -5,8 +5,8 @@
  *
  * License: BSD-3-Clause-LBNL
  */
-#ifndef PML_CURRENT_H_
-#define PML_CURRENT_H_
+#ifndef WARPX_PML_CURRENT_H_
+#define WARPX_PML_CURRENT_H_
 
 #include "BoundaryConditions/PMLComponent.H"
 
@@ -143,4 +143,4 @@ void damp_jz_pml (int j, int k, int l,
 #endif
 }
 
-#endif
+#endif //WARPX_PML_CURRENT_H_
diff --git a/Source/Diagnostics/BTD_Plotfile_Header_Impl.H b/Source/Diagnostics/BTD_Plotfile_Header_Impl.H
@@ -4,8 +4,8 @@
  *
  * License: BSD-3-Clause-LBNL
  */
-#ifndef BTD_PLOTFILE_HEADER_IMPL_H
-#define BTD_PLOTFILE_HEADER_IMPL_H
+#ifndef WARPX_BTD_PLOTFILE_HEADER_IMPL_H
+#define WARPX_BTD_PLOTFILE_HEADER_IMPL_H
 
 #include <AMReX_Array.H>
 #include <AMReX_Box.H>
@@ -342,4 +342,4 @@ public:
     std::string m_Header_path;
 };
 
-#endif
+#endif //WARPX_BTD_PLOTFILE_HEADER_IMPL_H
diff --git a/Source/Diagnostics/FlushFormats/FlushFormat.H b/Source/Diagnostics/FlushFormats/FlushFormat.H
@@ -5,7 +5,6 @@
 
 #include "Diagnostics/ParticleDiag/ParticleDiag.H"
 #include "Particles/MultiParticleContainer.H"
-#include "WarpX.H"
 
 class FlushFormat
 {

diff --git a/Source/EmbeddedBoundary/DistanceToEB.H b/Source/EmbeddedBoundary/DistanceToEB.H
@@ -4,8 +4,8 @@
  *
  * License: BSD-3-Clause-LBNL
  */
-#ifndef DISTANCETOEB_H_
-#define DISTANCETOEB_H_
+#ifndef WARPX_DISTANCETOEB_H_
+#define WARPX_DISTANCETOEB_H_
 
 #include "Utils/TextMsg.H"
 
@@ -129,4 +129,4 @@ amrex::RealVect interp_normal (int i, int j, int k, const amrex::Real W[AMREX_SP
 }
 
 #endif // AMREX_USE_EB
-#endif // DISTANCETOEB_H_
+#endif // WARPX_DISTANCETOEB_H_
diff --git a/Source/EmbeddedBoundary/ParticleBoundaryProcess.H b/Source/EmbeddedBoundary/ParticleBoundaryProcess.H
@@ -4,8 +4,8 @@
  *
  * License: BSD-3-Clause-LBNL
  */
-#ifndef PARTICLEBOUNDARYPROCESS_H_
-#define PARTICLEBOUNDARYPROCESS_H_
+#ifndef WARPX_PARTICLEBOUNDARYPROCESS_H_
+#define WARPX_PARTICLEBOUNDARYPROCESS_H_
 
 #include <AMReX_Particle.H>
 #include <AMReX_REAL.H>
@@ -36,4 +36,4 @@ struct Absorb {
 };
 }
 
-#endif
+#endif //WARPX_PARTICLEBOUNDARYPROCESS_H_
diff --git a/Source/EmbeddedBoundary/ParticleScraper.H b/Source/EmbeddedBoundary/ParticleScraper.H
@@ -4,8 +4,8 @@
  *
  * License: BSD-3-Clause-LBNL
  */
-#ifndef PARTICLESCRAPER_H_
-#define PARTICLESCRAPER_H_
+#ifndef WARPX_PARTICLESCRAPER_H_
+#define WARPX_PARTICLESCRAPER_H_
 
 #include "EmbeddedBoundary/DistanceToEB.H"
 #include "Particles/Pusher/GetAndSetPosition.H"
@@ -65,9 +65,9 @@
  */
 template <class PC, class F, std::enable_if_t<amrex::IsParticleContainer<PC>::value, int> foo = 0>
 void
-scrapeParticles (PC& pc, const amrex::Vector<const amrex::MultiFab*>& distance_to_eb, int lev, F&& f)
+scrapeParticlesAtEB (PC& pc, const amrex::Vector<const amrex::MultiFab*>& distance_to_eb, int lev, F&& f)
 {
-    scrapeParticles(pc, distance_to_eb, lev, lev, std::forward<F>(f));
+    scrapeParticlesAtEB(pc, distance_to_eb, lev, lev, std::forward<F>(f));
 }
 
 /**
@@ -108,9 +108,9 @@ scrapeParticles (PC& pc, const amrex::Vector<const amrex::MultiFab*>& distance_t
  */
 template <class PC, class F, std::enable_if_t<amrex::IsParticleContainer<PC>::value, int> foo = 0>
 void
-scrapeParticles (PC& pc, const amrex::Vector<const amrex::MultiFab*>& distance_to_eb, F&& f)
+scrapeParticlesAtEB (PC& pc, const amrex::Vector<const amrex::MultiFab*>& distance_to_eb, F&& f)
 {
-    scrapeParticles(pc, distance_to_eb, 0, pc.finestLevel(), std::forward<F>(f));
+    scrapeParticlesAtEB(pc, distance_to_eb, 0, pc.finestLevel(), std::forward<F>(f));
 }
 
 /**
@@ -153,10 +153,10 @@ scrapeParticles (PC& pc, const amrex::Vector<const amrex::MultiFab*>& distance_t
  */
 template <class PC, class F, std::enable_if_t<amrex::IsParticleContainer<PC>::value, int> foo = 0>
 void
-scrapeParticles (PC& pc, const amrex::Vector<const amrex::MultiFab*>& distance_to_eb,
+scrapeParticlesAtEB (PC& pc, const amrex::Vector<const amrex::MultiFab*>& distance_to_eb,
                  int lev_min, int lev_max, F&& f)
 {
-    BL_PROFILE("scrapeParticles");
+    BL_PROFILE("scrapeParticlesAtEB");
 
     for (int lev = lev_min; lev <= lev_max; ++lev)
     {
@@ -216,4 +216,4 @@ scrapeParticles (PC& pc, const amrex::Vector<const amrex::MultiFab*>& distance_t
     }
 }
 
-#endif
+#endif //WARPX_PARTICLESCRAPER_H_
diff --git a/Source/Evolve/WarpXEvolve.cpp b/Source/Evolve/WarpXEvolve.cpp
@@ -489,13 +489,7 @@ void WarpX::HandleParticlesAtBoundaries (int step, amrex::Real cur_time, int num
     mypc->ContinuousFluxInjection(cur_time, dt[0]);
 
     mypc->ApplyBoundaryConditions();
-
-    // interact the particles with EB walls (if present)
-#ifdef AMREX_USE_EB
-    mypc->ScrapeParticles(amrex::GetVecOfConstPtrs(m_distance_to_eb));
-#endif
-
-    m_particle_boundary_buffer->gatherParticles(*mypc, amrex::GetVecOfConstPtrs(m_distance_to_eb));
+    m_particle_boundary_buffer->gatherParticlesFromDomainBoundaries(*mypc);
 
     // Non-Maxwell solver: particles can move by an arbitrary number of cells
     if( electromagnetic_solver_id == ElectromagneticSolverAlgo::None ||
@@ -523,6 +517,13 @@ void WarpX::HandleParticlesAtBoundaries (int step, amrex::Real cur_time, int num
         }
     }
 
+    // interact the particles with EB walls (if present)
+#ifdef AMREX_USE_EB
+    mypc->ScrapeParticlesAtEB(amrex::GetVecOfConstPtrs(m_distance_to_eb));
+    m_particle_boundary_buffer->gatherParticlesFromEmbeddedBoundaries(*mypc, amrex::GetVecOfConstPtrs(m_distance_to_eb));
+    mypc->deleteInvalidParticles();
+#endif
+
     if (sort_intervals.contains(step+1)) {
         if (verbose) {
             amrex::Print() << Utils::TextMsg::Info("re-sorting particles");

diff --git a/Source/FieldSolver/ElectrostaticSolver.H b/Source/FieldSolver/ElectrostaticSolver.H
@@ -4,8 +4,8 @@
  *
  * License: BSD-3-Clause-LBNL
  */
-#ifndef ELECTROSTATICSOLVER_H_
-#define ELECTROSTATICSOLVER_H_
+#ifndef WARPX_ELECTROSTATICSOLVER_H_
+#define WARPX_ELECTROSTATICSOLVER_H_
 
 #include <AMReX_Array.H>
 #include <AMReX_Geometry.H>
@@ -122,4 +122,4 @@ namespace ElectrostaticSolver {
     };
 } // namespace ElectrostaticSolver
 
-#endif // ELECTROSTATICSOLVER_H_
+#endif // WARPX_ELECTROSTATICSOLVER_H_
diff --git a/Source/FieldSolver/FiniteDifferenceSolver/FiniteDifferenceAlgorithms/FieldAccessorFunctors.H b/Source/FieldSolver/FiniteDifferenceSolver/FiniteDifferenceAlgorithms/FieldAccessorFunctors.H
@@ -8,11 +8,9 @@
 #ifndef WARPX_FIELD_ACCESSOR_FUNCTORS_H
 #define WARPX_FIELD_ACCESSOR_FUNCTORS_H
 
-#include "WarpX.H"
-#include "FieldSolver/FiniteDifferenceSolver/MacroscopicProperties/MacroscopicProperties.H"
-
 #include <AMReX_Array.H>
-
+#include <AMReX_Extension.H>
+#include <AMReX_Gpu.H>
 
 /**
  * \brief Functor that returns the division of the source m_field Array4 value

diff --git a/Source/FieldSolver/MagnetostaticSolver/MagnetostaticSolver.H b/Source/FieldSolver/MagnetostaticSolver/MagnetostaticSolver.H
@@ -4,8 +4,8 @@
  *
  * License: BSD-3-Clause-LBNL
  */
-#ifndef MAGNETOSTATICSOLVER_H_
-#define MAGNETOSTATICSOLVER_H_
+#ifndef WARPX_MAGNETOSTATICSOLVER_H_
+#define WARPX_MAGNETOSTATICSOLVER_H_
 
 #include <AMReX_Array.H>
 #include <AMReX_MultiFab.H>
@@ -54,4 +54,4 @@ namespace MagnetostaticSolver {
     };
 } // namespace MagnetostaticSolver
 
-#endif //MAGNETOSTATICSOLVER_H_
+#endif //WARPX_MAGNETOSTATICSOLVER_H_
diff --git a/Source/FieldSolver/WarpXPushFieldsEM_K.H b/Source/FieldSolver/WarpXPushFieldsEM_K.H
@@ -5,8 +5,8 @@
  * License: BSD-3-Clause-LBNL
  */
 
-#ifndef WarpXPushFieldsEM_K_h
-#define WarpXPushFieldsEM_K_h
+#ifndef WARPX_PushFieldsEM_K_h
+#define WARPX_PushFieldsEM_K_h
 
 #include "Utils/WarpXConst.H"
 
@@ -117,4 +117,4 @@ void damp_field_in_guards(
     }
 }
 
-#endif
+#endif //WARPX_PushFieldsEM_K_h
diff --git a/Source/FieldSolver/WarpX_QED_K.H b/Source/FieldSolver/WarpX_QED_K.H
@@ -5,8 +5,8 @@
  * License: BSD-3-Clause-LBNL
  */
 
-#ifndef WarpX_QED_K_h
-#define WarpX_QED_K_h
+#ifndef WARPX_QED_K_h
+#define WARPX_QED_K_h
 
 #include "Utils/WarpXConst.H"
 
@@ -359,4 +359,4 @@ const amrex::Real dyi = 1._rt/dy;
 
 }
 
-#endif
+#endif //WARPX_QED_K_h
diff --git a/Source/Fluids/MultiFluidContainer_fwd.H b/Source/Fluids/MultiFluidContainer_fwd.H
@@ -6,6 +6,7 @@
  */
 
 #ifndef WARPX_MultiFluidContainer_fwd_H_
+#define WARPX_MultiFluidContainer_fwd_H_
 
 class MultiFluidContainer;
 

diff --git a/Source/Fluids/WarpXFluidContainer_fwd.H b/Source/Fluids/WarpXFluidContainer_fwd.H
@@ -6,6 +6,7 @@
  */
 
 #ifndef WARPX_WarpXFluidContainer_fwd_H_
+#define WARPX_WarpXFluidContainer_fwd_H_
 
 class WarpXFluidContainer;
 

diff --git a/Source/Initialization/ExternalField.H b/Source/Initialization/ExternalField.H
@@ -5,8 +5,8 @@
  *
  * License: BSD-3-Clause-LBNL
  */
-#ifndef EXTERNAL_FIELD_H_
-#define EXTERNAL_FIELD_H_
+#ifndef WARPX_EXTERNAL_FIELD_H_
+#define WARPX_EXTERNAL_FIELD_H_
 
 #include "ExternalField_fwd.H"
 
@@ -66,4 +66,4 @@ struct ExternalFieldParams
     std::string external_fields_path;
 };
 
-#endif //EXTERNAL_FIELD_H_
+#endif //WARPX_EXTERNAL_FIELD_H_
diff --git a/Source/Initialization/ExternalField_fwd.H b/Source/Initialization/ExternalField_fwd.H
@@ -5,9 +5,9 @@
  *
  * License: BSD-3-Clause-LBNL
  */
-#ifndef EXTERNAL_FIELD_FWD_H_
-#define EXTERNAL_FIELD_FWD_H_
+#ifndef WARPX_EXTERNAL_FIELD_FWD_H_
+#define WARPX_EXTERNAL_FIELD_FWD_H_
 
 struct ExternalFieldParams;
 
-#endif //EXTERNAL_FIELD_FWD_H_
+#endif //WARPX_EXTERNAL_FIELD_FWD_H_
diff --git a/Source/Initialization/GetTemperature.H b/Source/Initialization/GetTemperature.H
@@ -6,8 +6,8 @@
  * License: BSD-3-Clause-LBNL
  */
 
-#ifndef GET_TEMPERATURE_H_
-#define GET_TEMPERATURE_H_
+#ifndef WARPX_GET_TEMPERATURE_H_
+#define WARPX_GET_TEMPERATURE_H_
 
 #include "TemperatureProperties.H"
 
@@ -69,4 +69,4 @@ struct GetTemperature
         }
     }
 };
-#endif
+#endif //WARPX_GET_TEMPERATURE_H_
diff --git a/Source/Initialization/GetVelocity.H b/Source/Initialization/GetVelocity.H
@@ -5,8 +5,8 @@
  * License: BSD-3-Clause-LBNL
  */
 
-#ifndef GET_VELOCITY_H_
-#define GET_VELOCITY_H_
+#ifndef WARPX_GET_VELOCITY_H_
+#define WARPX_GET_VELOCITY_H_
 
 #include "VelocityProperties.H"
 
@@ -86,4 +86,4 @@ struct GetVelocity
         return m_dir;
     }
 };
-#endif
+#endif //WARPX_GET_VELOCITY_H_
diff --git a/Source/Initialization/InjectorDensity.H b/Source/Initialization/InjectorDensity.H
@@ -6,8 +6,8 @@
  *
  * License: BSD-3-Clause-LBNL
  */
-#ifndef INJECTOR_DENSITY_H_
-#define INJECTOR_DENSITY_H_
+#ifndef WARPX_INJECTOR_DENSITY_H_
+#define WARPX_INJECTOR_DENSITY_H_
 
 #include "Utils/WarpXConst.H"
 
@@ -218,4 +218,4 @@ struct InjectorDensityDeleter {
     }
 };
 
-#endif
+#endif //WARPX_INJECTOR_DENSITY_H_
diff --git a/Source/Initialization/InjectorFlux.H b/Source/Initialization/InjectorFlux.H
@@ -4,8 +4,8 @@
  *
  * License: BSD-3-Clause-LBNL
  */
-#ifndef INJECTOR_FLUX_H_
-#define INJECTOR_FLUX_H_
+#ifndef WARPX_INJECTOR_FLUX_H_
+#define WARPX_INJECTOR_FLUX_H_
 
 #include "Utils/WarpXConst.H"
 
@@ -149,4 +149,4 @@ struct InjectorFluxDeleter {
     }
 };
 
-#endif
+#endif //WARPX_INJECTOR_FLUX_H_
-Original file line number
+Diff line change
@@ Expand Up / @@ -6,6 +6,7 @@ @@
      */
     #ifndef WARPX_MultiFluidContainer_fwd_H_
+    #define WARPX_MultiFluidContainer_fwd_H_
     class MultiFluidContainer;
@@ Expand Down @@