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

…anitizer

.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 1f038e767011e20100af6ab0db02c69cf7ebe55c && cd -
+        cd ../amrex && git checkout --detach 259db7cfb99e7d1d2ab4bec9b1587fdf624a138a && 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/usage/parameters.rst

@@ -581,11 +581,26 @@ Additional PML parameters
 Embedded Boundary Conditions
 ----------------------------
 
-* ``warpx.eb_implicit_function`` (`string`)
-    A function of `x`, `y`, `z` that defines the surface of the embedded
-    boundary. That surface lies where the function value is 0 ;
-    the physics simulation area is where the function value is negative ;
-    the interior of the embeddded boundary is where the function value is positive.
+In WarpX, the embedded boundary can be defined in either of two ways:
+
+    - **From an analytical function:**
+        In that case, you will need to set the following parameter in the input file.
+
+        * ``warpx.eb_implicit_function`` (`string`)
+            A function of `x`, `y`, `z` that defines the surface of the embedded
+            boundary. That surface lies where the function value is 0 ;
+            the physics simulation area is where the function value is negative ;
+            the interior of the embeddded boundary is where the function value is positive.
+
+    - **From an STL file:**
+        In that case, you will need to set the following parameters in the input file.
+
+        * ``eb2.stl_file`` (`string`)
+            The path to an STL file. In addition, you also need to set ``eb2.geom_type = stl``,
+            in order for the file to be read by WarpX.
+
+Whether the embedded boundary is defined with an analytical function or an STL file, you can
+additionally define the electric potential at the embedded boundary with an analytical function:
 
 * ``warpx.eb_potential(x,y,z,t)`` (`string`)
     Gives the value of the electric potential at the surface of the embedded boundary,
@@ -2431,7 +2446,7 @@ Grid types (collocated, staggered, hybrid)
     For example, :math:`E_z` is gathered using ``algo.particle_shape`` along :math:`(x,y)` and ``algo.particle_shape - 1`` along :math:`z`.
     See equations (21)-(23) of :cite:t:`param-Godfrey2013` and associated references for details.
 
-    Default: ``interpolation.galerkin_scheme = 0`` with collocated grids and/or momentum-conserving field gathering, ``interpolation.galerkin_scheme = 1`` otherwise.
+    Default: ``interpolation.galerkin_scheme = 0`` with collocated grids, or momentum-conserving field gathering, or when ``algo.current_deposition = direct`` ; ``interpolation.galerkin_scheme = 1`` otherwise.
 
     .. warning::
 

Examples/Tests/collision/inputs_3d

@@ -22,6 +22,7 @@ boundary.field_hi = periodic periodic periodic
 warpx.serialize_initial_conditions = 1
 warpx.verbose = 1
 warpx.const_dt = 1.224744871e-07
+warpx.random_seed = 2034958209
 
 # Do not evolve the E and B fields
 algo.maxwell_solver = none

Regression/Checksum/benchmarks_json/Langmuir_multi_2d_MR_psatd.json

@@ -1,40 +1,40 @@
 {
-  "electrons": {
-    "particle_momentum_x": 4.2387000553111037e-20,
-    "particle_momentum_y": 0.0,
-    "particle_momentum_z": 4.238700039223283e-20,
-    "particle_position_x": 0.6553599659707846,
-    "particle_position_y": 0.6553599659699976,
-    "particle_weight": 3200000000000000.5
-  },
   "lev=0": {
     "Bx": 0.0,
-    "By": 46.86760020196344,
+    "By": 46.65494014556924,
     "Bz": 0.0,
-    "Ex": 7589330186947.288,
+    "Ex": 7596470155558.35,
     "Ey": 0.0,
-    "Ez": 7589330198843.742,
-    "jx": 7283102663077210.0,
+    "Ez": 7596470167219.471,
+    "jx": 7277974695617658.0,
     "jy": 0.0,
-    "jz": 7283102630279985.0
+    "jz": 7277974664068728.0
   },
   "lev=1": {
     "Bx": 0.0,
-    "By": 369.2209081024592,
+    "By": 371.2497742366917,
     "Bz": 0.0,
-    "Ex": 7593801203430.788,
+    "Ex": 7596619292118.433,
     "Ey": 0.0,
-    "Ez": 7593800988021.711,
-    "jx": 6597471633118175.0,
+    "Ez": 7596619076137.7295,
+    "jx": 6592788899529852.0,
     "jy": 0.0,
-    "jz": 6597471447306984.0
+    "jz": 6592788734672843.0
+  },
+  "electrons": {
+    "particle_momentum_x": 4.2314133085678375e-20,
+    "particle_momentum_y": 0.0,
+    "particle_momentum_z": 4.2314132920088513e-20,
+    "particle_position_x": 0.6553599899254421,
+    "particle_position_y": 0.6553599899246253,
+    "particle_weight": 3200000000000000.5
   },
   "positrons": {
-    "particle_momentum_x": 4.238670783273887e-20,
+    "particle_momentum_x": 4.2314444192249906e-20,
     "particle_momentum_y": 0.0,
-    "particle_momentum_z": 4.238670762294589e-20,
-    "particle_position_x": 0.6553596917214832,
-    "particle_position_y": 0.6553596917221793,
+    "particle_momentum_z": 4.231444401040395e-20,
+    "particle_position_x": 0.655359770013864,
+    "particle_position_y": 0.6553597700144888,
     "particle_weight": 3200000000000000.5
   }
 }

Regression/Checksum/benchmarks_json/Langmuir_multi_2d_psatd.json

@@ -1,27 +1,27 @@
 {
-  "electrons": {
-    "particle_momentum_x": 5.663705661977914e-20,
-    "particle_momentum_y": 0.0,
-    "particle_momentum_z": 5.663705661977915e-20,
-    "particle_position_x": 0.65536,
-    "particle_position_y": 0.6553599999999999,
-    "particle_weight": 3200000000000000.5
-  },
   "lev=0": {
-    "Ex": 3771082811318.298,
+    "Ex": 3751590727260.198,
     "Ey": 0.0,
-    "Ez": 3771082811318.301,
-    "jx": 1.009365330460902e+16,
+    "Ez": 3751590727260.1885,
+    "jx": 1.0100623838390416e+16,
     "jy": 0.0,
-    "jz": 1.009365330460902e+16,
+    "jz": 1.0100623838390416e+16,
     "part_per_cell": 131072.0
   },
   "positrons": {
-    "particle_momentum_x": 5.663705661977916e-20,
+    "particle_momentum_x": 5.668407775012392e-20,
     "particle_momentum_y": 0.0,
-    "particle_momentum_z": 5.663705661977916e-20,
+    "particle_momentum_z": 5.668407775012392e-20,
     "particle_position_x": 0.65536,
     "particle_position_y": 0.65536,
     "particle_weight": 3200000000000000.5
+  },
+  "electrons": {
+    "particle_momentum_x": 5.668407775012391e-20,
+    "particle_momentum_y": 0.0,
+    "particle_momentum_z": 5.668407775012391e-20,
+    "particle_position_x": 0.65536,
+    "particle_position_y": 0.6553600000000002,
+    "particle_weight": 3200000000000000.5
   }
 }

Regression/Checksum/benchmarks_json/Langmuir_multi_2d_psatd_multiJ.json

@@ -1,29 +1,29 @@
 {
-  "electrons": {
-    "particle_momentum_x": 5.663705657675969e-20,
-    "particle_momentum_y": 0.0,
-    "particle_momentum_z": 5.663705657675969e-20,
-    "particle_position_x": 0.65536,
-    "particle_position_y": 0.65536,
-    "particle_weight": 3200000000000000.5
-  },
   "lev=0": {
     "Bx": 0.0,
-    "By": 3.4892704618136277,
+    "By": 5.710236645367475,
     "Bz": 0.0,
-    "Ex": 3771082786646.7104,
+    "Ex": 3751590785149.1333,
     "Ey": 0.0,
-    "Ez": 3771082786646.702,
-    "jx": 1.0093631772735916e+16,
+    "Ez": 3751590785149.124,
+    "jx": 1.0100602372860838e+16,
     "jy": 0.0,
-    "jz": 1.0093631772735912e+16
+    "jz": 1.0100602372860836e+16
   },
   "positrons": {
-    "particle_momentum_x": 5.663705657675971e-20,
+    "particle_momentum_x": 5.668407759026453e-20,
     "particle_momentum_y": 0.0,
-    "particle_momentum_z": 5.663705657675969e-20,
-    "particle_position_x": 0.65536,
+    "particle_momentum_z": 5.668407759026454e-20,
+    "particle_position_x": 0.6553599999999999,
     "particle_position_y": 0.65536,
     "particle_weight": 3200000000000000.5
+  },
+  "electrons": {
+    "particle_momentum_x": 5.668407759026452e-20,
+    "particle_momentum_y": 0.0,
+    "particle_momentum_z": 5.668407759026452e-20,
+    "particle_position_x": 0.65536,
+    "particle_position_y": 0.6553600000000002,
+    "particle_weight": 3200000000000000.5
   }
 }

Regression/Checksum/benchmarks_json/Langmuir_multi_psatd_div_cleaning.json

@@ -1,30 +1,30 @@
 {
-  "electrons": {
-    "particle_momentum_x": 9.520485222844096e-20,
-    "particle_position_x": 2.6214400000233367,
-    "particle_position_y": 2.6214400000233367,
-    "particle_position_z": 2.6214400000000007,
-    "particle_weight": 128000000000.00002
-  },
   "lev=0": {
-    "Bx": 78.90261993791012,
-    "By": 78.90261993794903,
-    "Bz": 78.9041393998435,
-    "Ex": 84580428018688.97,
-    "Ey": 84580428018688.73,
-    "Ez": 84580441923246.2,
-    "F": 685.6927382678912,
-    "divE": 7.94184911020468e+19,
-    "jx": 6.007457695701311e+16,
-    "jy": 6.007457695701312e+16,
-    "jz": 6.007453636158103e+16,
+    "Bx": 86.03228226677659,
+    "By": 86.03228226679013,
+    "Bz": 86.033798606458,
+    "Ex": 84659309211473.42,
+    "Ey": 84659309211473.42,
+    "Ez": 84659323064827.52,
+    "F": 700.2020613746595,
+    "divE": 7.94984970149747e+19,
+    "jx": 5.999100369888243e+16,
+    "jy": 5.999100369888247e+16,
+    "jz": 5.999096310379822e+16,
     "part_per_cell": 524288.0,
-    "rho": 705198439.2596256
+    "rho": 705877712.4251474
   },
   "positrons": {
-    "particle_momentum_z": 9.520479438980041e-20,
-    "particle_position_x": 2.6214400000233367,
-    "particle_position_y": 2.6214400000233358,
+    "particle_momentum_z": 9.508931687286131e-20,
+    "particle_position_x": 2.621440000034161,
+    "particle_position_y": 2.6214400000341618,
     "particle_position_z": 2.62144
+  },
+  "electrons": {
+    "particle_momentum_x": 9.508937471997448e-20,
+    "particle_position_x": 2.6214400000341604,
+    "particle_position_y": 2.621440000034161,
+    "particle_position_z": 2.6214399999999993,
+    "particle_weight": 128000000000.00002
   }
-}
+}

Regression/Checksum/benchmarks_json/Langmuir_multi_psatd_multiJ.json

@@ -1,28 +1,28 @@
 {
-  "electrons": {
-    "particle_momentum_x": 9.633869745818886e-20,
-    "particle_position_x": 2.621440000001177,
-    "particle_position_y": 2.6214400000011784,
-    "particle_position_z": 2.6214400000000007,
-    "particle_weight": 128000000000.00002
-  },
   "lev=0": {
-    "Bx": 80.96035538655111,
-    "By": 80.96035538657691,
-    "Bz": 80.96271445263956,
-    "Ex": 84777489275096.88,
-    "Ey": 84777489275096.88,
-    "Ez": 84777485856239.4,
-    "jx": 6.08447015360442e+16,
-    "jy": 6.084470153604425e+16,
-    "jz": 6.084470085554113e+16,
+    "Bx": 88.73949682623977,
+    "By": 88.73949682627456,
+    "Bz": 88.74185838578241,
+    "Ex": 84851140116479.64,
+    "Ey": 84851140116479.62,
+    "Ez": 84851136696893.72,
+    "jx": 6.075773528102969e+16,
+    "jy": 6.0757735281029736e+16,
+    "jz": 6.075773460167053e+16,
     "part_per_cell": 524288.0,
-    "rho": 703546536.8089281
+    "rho": 704298346.5173542
   },
   "positrons": {
-    "particle_momentum_z": 9.63386961193585e-20,
-    "particle_position_x": 2.621440000001177,
-    "particle_position_y": 2.621440000001179,
-    "particle_position_z": 2.6214400000000007
+    "particle_momentum_z": 9.621748455552108e-20,
+    "particle_position_x": 2.621440000001309,
+    "particle_position_y": 2.6214400000013076,
+    "particle_position_z": 2.6214399999999998
+  },
+  "electrons": {
+    "particle_momentum_x": 9.621748589257923e-20,
+    "particle_position_x": 2.621440000001309,
+    "particle_position_y": 2.6214400000013076,
+    "particle_position_z": 2.6214399999999998,
+    "particle_weight": 128000000000.00002
   }
 }

Regression/Checksum/benchmarks_json/Python_Langmuir.json

@@ -1,13 +1,13 @@
 {
+  "lev=0": {
+    "Ex": 3047094224871324.5,
+    "jx": 3.294250379355652e+18
+  },
   "electrons": {
-    "particle_momentum_x": 1.7507165884671642e-17,
-    "particle_position_x": 10.350911572498216,
-    "particle_position_y": 10.485760000000003,
-    "particle_position_z": 10.485760000000003,
+    "particle_momentum_x": 1.740964347107983e-17,
+    "particle_position_x": 10.351045542291539,
+    "particle_position_y": 10.485759999999997,
+    "particle_position_z": 10.48576,
     "particle_weight": 320000000000.00006
-  },
-  "lev=0": {
-    "Ex": 3091324128949712.5,
-    "jx": 3.3015975627803766e+18
   }
 }

Regression/Checksum/benchmarks_json/Python_Langmuir_2d.json

@@ -1,12 +1,12 @@
 {
+  "lev=0": {
+    "Ex": 53556162492188.62,
+    "jx": 5.722548841990386e+16
+  },
   "electrons": {
-    "particle_momentum_x": 1.0449418710231497e-19,
-    "particle_position_x": 0.0831205701527011,
-    "particle_position_y": 0.08192,
+    "particle_momentum_x": 1.0581442023547547e-19,
+    "particle_position_x": 0.0831038802568349,
+    "particle_position_y": 0.08191999999999999,
     "particle_weight": 8000000000000001.0
-  },
-  "lev=0": {
-    "Ex": 54311177004701.516,
-    "jx": 5.639670983525456e+16
   }
 }